Starting phenix.real_space_refine on Fri Feb 16 02:58:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufi_42208/02_2024/8ufi_42208_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufi_42208/02_2024/8ufi_42208.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufi_42208/02_2024/8ufi_42208_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufi_42208/02_2024/8ufi_42208_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufi_42208/02_2024/8ufi_42208_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufi_42208/02_2024/8ufi_42208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufi_42208/02_2024/8ufi_42208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufi_42208/02_2024/8ufi_42208_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufi_42208/02_2024/8ufi_42208_updated.pdb" } resolution = 3.1 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= 0.045 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 99 5.16 5 C 9035 2.51 5 N 2381 2.21 5 O 2636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 444": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 80": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14157 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6682 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 31, 'TRANS': 784} Chain: "B" Number of atoms: 6678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 6678 Classifications: {'peptide': 821} Link IDs: {'PTRANS': 32, 'TRANS': 788} Chain: "C" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 368 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 5, 'TRANS': 42} Chain breaks: 2 Chain: "D" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 379 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 5, 'TRANS': 43} Chain breaks: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.76, per 1000 atoms: 0.55 Number of scatterers: 14157 At special positions: 0 Unit cell: (94.094, 118.91, 165.44, 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 99 16.00 P 2 15.00 Mg 2 11.99 O 2636 8.00 N 2381 7.00 C 9035 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: 5.99 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 599 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" ND1 HIS B 597 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 561 " 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3296 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 4 sheets defined 52.5% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 8 through 15 removed outlier: 3.873A pdb=" N LEU A 13 " --> pdb=" O GLU A 10 " (cutoff:3.500A) 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 67 removed outlier: 3.769A pdb=" N ASP A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 121 through 124 No H-bonds generated for 'chain 'A' and resid 121 through 124' Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 205 through 248 removed outlier: 4.303A pdb=" N ASN A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 265 Processing helix chain 'A' and resid 288 through 295 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: 3.649A pdb=" N VAL A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASN A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' 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 528 Processing helix chain 'A' and resid 531 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 580 through 583 removed outlier: 3.531A pdb=" N TYR A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 583' Processing helix chain 'A' and resid 586 through 597 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 652 through 669 removed outlier: 3.544A pdb=" N THR A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 690 removed outlier: 5.391A pdb=" N THR A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N MET A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 703 removed outlier: 3.744A pdb=" N LEU A 703 " --> pdb=" O GLN A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 720 Processing helix chain 'A' and resid 722 through 725 No H-bonds generated for 'chain 'A' and resid 722 through 725' Processing helix chain 'A' and resid 728 through 752 removed outlier: 4.592A pdb=" N LYS A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 779 Proline residue: A 770 - end of helix Processing helix chain 'A' and resid 781 through 791 Processing helix chain 'A' and resid 793 through 820 Proline residue: A 797 - end of helix Processing helix chain 'B' and resid 9 through 14 Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 48 through 67 Processing helix chain 'B' and resid 72 through 87 removed outlier: 3.611A pdb=" N SER B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) 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 163 through 167 Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 214 through 248 Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 265 through 268 No H-bonds generated for 'chain 'B' and resid 265 through 268' Processing helix chain 'B' and resid 286 through 294 Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 338 through 341 No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 412 through 456 removed outlier: 4.660A pdb=" N LEU B 430 " --> pdb=" O GLY B 426 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN B 431 " --> pdb=" O TRP B 427 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 465 Processing helix chain 'B' and resid 482 through 492 Processing helix chain 'B' and resid 513 through 526 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 560 through 574 removed outlier: 5.900A pdb=" N VAL B 565 " --> pdb=" O HIS B 561 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 566 " --> pdb=" O GLY B 562 " (cutoff:3.500A) 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 removed outlier: 3.536A pdb=" N MET B 610 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 619 Processing helix chain 'B' and resid 624 through 638 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: 3.741A 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 676 through 688 removed outlier: 3.726A pdb=" N LYS B 687 " --> pdb=" O VAL B 683 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN B 688 " --> pdb=" O ASP B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 701 removed outlier: 3.917A pdb=" N LEU B 701 " --> pdb=" O GLU B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 718 Processing helix chain 'B' and resid 726 through 750 removed outlier: 4.276A pdb=" N LYS B 731 " --> pdb=" O GLU B 727 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 734 " --> pdb=" O SER B 730 " (cutoff:3.500A) 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 823 Proline residue: B 795 - end of helix removed outlier: 4.413A pdb=" N ARG B 799 " --> pdb=" O MET B 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 78 through 83 Processing sheet with id= A, first strand: chain 'A' and resid 106 through 112 removed outlier: 6.656A pdb=" N LEU A 96 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 189 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 11.362A pdb=" N ALA A 101 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 14.050A pdb=" N ASP A 187 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 182 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE A 191 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER A 180 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET A 193 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 178 " --> pdb=" O MET A 193 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 357 through 360 removed outlier: 3.884A pdb=" N LYS A 317 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 110 removed outlier: 6.422A pdb=" N LEU B 94 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 91 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 187 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N GLN B 99 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 13.909A pdb=" N ASP B 185 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE B 180 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL B 189 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR B 178 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N MET B 191 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 176 " --> pdb=" O MET B 191 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 328 through 331 removed outlier: 7.026A pdb=" N LEU B 277 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL B 316 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL B 275 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASP B 318 " --> pdb=" O TYR B 273 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR B 273 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 396 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 388 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL B 398 " --> pdb=" O MET B 386 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N MET B 386 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 400 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 384 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR B 402 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN B 382 " --> pdb=" O TYR B 402 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1725 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: 4.17 Time building geometry restraints manager: 6.41 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: 2416 1.31 - 1.44: 3763 1.44 - 1.56: 8116 1.56 - 1.69: 6 1.69 - 1.82: 172 Bond restraints: 14473 Sorted by residual: bond pdb=" C6 PCG A 901 " pdb=" O6 PCG A 901 " ideal model delta sigma weight residual 1.220 1.184 0.036 2.00e-02 2.50e+03 3.25e+00 bond pdb=" C6 PCG B 901 " pdb=" O6 PCG B 901 " ideal model delta sigma weight residual 1.220 1.185 0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" O1A PCG A 901 " pdb=" PA PCG A 901 " ideal model delta sigma weight residual 1.681 1.647 0.034 2.00e-02 2.50e+03 2.94e+00 bond pdb=" O1A PCG B 901 " pdb=" PA PCG B 901 " ideal model delta sigma weight residual 1.681 1.647 0.034 2.00e-02 2.50e+03 2.91e+00 bond pdb=" CB ASP B 752 " pdb=" CG ASP B 752 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.35e+00 ... (remaining 14468 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.02: 323 106.02 - 113.01: 7678 113.01 - 120.01: 5090 120.01 - 127.00: 6301 127.00 - 134.00: 169 Bond angle restraints: 19561 Sorted by residual: angle pdb=" N ILE A 795 " pdb=" CA ILE A 795 " pdb=" C ILE A 795 " ideal model delta sigma weight residual 112.29 108.61 3.68 9.40e-01 1.13e+00 1.53e+01 angle pdb=" C ASP B 824 " pdb=" N GLN B 825 " pdb=" CA GLN B 825 " ideal model delta sigma weight residual 121.54 128.95 -7.41 1.91e+00 2.74e-01 1.50e+01 angle pdb=" CA GLN A 285 " pdb=" CB GLN A 285 " pdb=" CG GLN A 285 " ideal model delta sigma weight residual 114.10 121.37 -7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" CB LYS A 186 " pdb=" CG LYS A 186 " pdb=" CD LYS A 186 " ideal model delta sigma weight residual 111.30 119.13 -7.83 2.30e+00 1.89e-01 1.16e+01 angle pdb=" CB GLN C 34 " pdb=" CG GLN C 34 " pdb=" CD GLN C 34 " ideal model delta sigma weight residual 112.60 118.27 -5.67 1.70e+00 3.46e-01 1.11e+01 ... (remaining 19556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7379 17.83 - 35.66: 1035 35.66 - 53.50: 263 53.50 - 71.33: 48 71.33 - 89.16: 20 Dihedral angle restraints: 8745 sinusoidal: 3660 harmonic: 5085 Sorted by residual: dihedral pdb=" CA GLY B 562 " pdb=" C GLY B 562 " pdb=" N PHE B 563 " pdb=" CA PHE B 563 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 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 180.00 161.12 18.88 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ALA A 303 " pdb=" C ALA A 303 " pdb=" N GLY A 304 " pdb=" CA GLY A 304 " ideal model delta harmonic sigma weight residual 180.00 -161.71 -18.29 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 8742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1412 0.032 - 0.064: 494 0.064 - 0.096: 154 0.096 - 0.128: 61 0.128 - 0.160: 4 Chirality restraints: 2125 Sorted by residual: chirality pdb=" CB ILE C 54 " pdb=" CA ILE C 54 " pdb=" CG1 ILE C 54 " pdb=" CG2 ILE C 54 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CB ILE B 662 " pdb=" CA ILE B 662 " pdb=" CG1 ILE B 662 " pdb=" CG2 ILE B 662 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CB VAL A 454 " pdb=" CA VAL A 454 " pdb=" CG1 VAL A 454 " pdb=" CG2 VAL A 454 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 2122 not shown) Planarity restraints: 2526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 752 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ASP B 752 " 0.055 2.00e-02 2.50e+03 pdb=" O ASP B 752 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN B 753 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 433 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO A 434 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 434 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 434 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 444 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" CD GLU A 444 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU A 444 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 444 " -0.010 2.00e-02 2.50e+03 ... (remaining 2523 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 111 2.54 - 3.13: 11049 3.13 - 3.72: 23547 3.72 - 4.31: 32122 4.31 - 4.90: 54361 Nonbonded interactions: 121190 Sorted by model distance: nonbonded pdb=" OD2 ASP A 600 " pdb="ZN ZN A 902 " model vdw 1.947 2.230 nonbonded pdb=" OD1 ASP A 720 " pdb="ZN ZN A 902 " model vdw 1.957 2.230 nonbonded pdb=" OD1 ASP A 600 " pdb="MG MG A 903 " model vdw 2.062 2.170 nonbonded pdb=" OG SER A 246 " pdb=" O PHE D 38 " model vdw 2.164 2.440 nonbonded pdb=" O ASN A 504 " pdb=" OG1 THR A 577 " model vdw 2.200 2.440 ... (remaining 121185 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' selection = (chain 'D' and resid 12 through 86) } 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: 1.520 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: 9.310 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 42.290 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 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 0.038 14473 Z= 0.175 Angle : 0.548 7.833 19561 Z= 0.299 Chirality : 0.038 0.160 2125 Planarity : 0.004 0.043 2526 Dihedral : 17.770 89.162 5449 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.49 % Favored : 96.33 % Rotamer: Outliers : 0.19 % Allowed : 18.97 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.21), residues: 1718 helix: 1.89 (0.17), residues: 950 sheet: 0.21 (0.46), residues: 142 loop : 0.30 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 561 HIS 0.004 0.001 HIS A 660 PHE 0.009 0.001 PHE B 588 TYR 0.014 0.001 TYR B 783 ARG 0.011 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8857 (mtp) cc_final: 0.8509 (mtp) REVERT: B 72 MET cc_start: 0.8940 (tmm) cc_final: 0.8667 (tmm) REVERT: B 307 ASP cc_start: 0.8468 (t0) cc_final: 0.8238 (t0) REVERT: D 11 ARG cc_start: 0.8377 (tmm-80) cc_final: 0.8010 (ptm-80) outliers start: 3 outliers final: 2 residues processed: 120 average time/residue: 0.3231 time to fit residues: 55.5390 Evaluate side-chains 118 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain D residue 53 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 0.0870 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 743 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: 0.8923 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14473 Z= 0.321 Angle : 0.543 6.985 19561 Z= 0.283 Chirality : 0.040 0.148 2125 Planarity : 0.004 0.042 2526 Dihedral : 4.033 23.619 1895 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.90 % Favored : 95.87 % Rotamer: Outliers : 1.81 % Allowed : 18.26 % Favored : 79.94 % 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: 1.59 (0.21), residues: 1718 helix: 1.73 (0.17), residues: 967 sheet: 0.12 (0.44), residues: 143 loop : 0.33 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 561 HIS 0.007 0.001 HIS B 561 PHE 0.012 0.001 PHE A 19 TYR 0.016 0.001 TYR B 97 ARG 0.005 0.000 ARG D 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8938 (mtp) cc_final: 0.8398 (mtt) REVERT: A 94 MET cc_start: 0.8817 (mtp) cc_final: 0.8249 (mtp) REVERT: A 440 MET cc_start: 0.9168 (mmm) cc_final: 0.8770 (mmm) REVERT: A 444 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8578 (tm-30) REVERT: C 29 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8464 (mptt) outliers start: 28 outliers final: 17 residues processed: 135 average time/residue: 0.3031 time to fit residues: 59.3155 Evaluate side-chains 132 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 660 MET Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 138 optimal weight: 0.2980 chunk 154 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 52 GLN ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8897 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14473 Z= 0.170 Angle : 0.475 6.689 19561 Z= 0.250 Chirality : 0.039 0.146 2125 Planarity : 0.004 0.037 2526 Dihedral : 3.900 22.108 1891 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.38 % Favored : 96.45 % Rotamer: Outliers : 2.32 % Allowed : 18.06 % 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: 1.58 (0.21), residues: 1718 helix: 1.71 (0.17), residues: 964 sheet: 0.17 (0.44), residues: 143 loop : 0.34 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 561 HIS 0.006 0.001 HIS B 658 PHE 0.015 0.001 PHE A 19 TYR 0.013 0.001 TYR B 273 ARG 0.004 0.000 ARG D 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8978 (mtp) cc_final: 0.8466 (mtt) REVERT: A 94 MET cc_start: 0.8899 (mtp) cc_final: 0.8214 (mtp) REVERT: A 183 MET cc_start: 0.9078 (mtp) cc_final: 0.8261 (mmm) REVERT: A 440 MET cc_start: 0.9158 (mmm) cc_final: 0.8731 (mmm) REVERT: A 444 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8478 (tm-30) REVERT: B 661 ASP cc_start: 0.9169 (m-30) cc_final: 0.8934 (m-30) REVERT: C 17 MET cc_start: 0.7844 (mmt) cc_final: 0.7581 (mmm) REVERT: C 29 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8448 (mptt) REVERT: D 11 ARG cc_start: 0.8505 (tmm-80) cc_final: 0.8027 (ptm-80) REVERT: D 24 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8413 (ttp80) outliers start: 36 outliers final: 18 residues processed: 144 average time/residue: 0.3116 time to fit residues: 65.0158 Evaluate side-chains 133 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 660 MET Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 74 optimal weight: 0.1980 chunk 104 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 147 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 HIS ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 52 GLN ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14473 Z= 0.171 Angle : 0.473 6.304 19561 Z= 0.246 Chirality : 0.039 0.217 2125 Planarity : 0.004 0.035 2526 Dihedral : 3.834 21.890 1891 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.16 % Rotamer: Outliers : 2.13 % Allowed : 18.32 % Favored : 79.55 % 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: 1.62 (0.21), residues: 1718 helix: 1.73 (0.17), residues: 966 sheet: 0.18 (0.44), residues: 143 loop : 0.37 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 561 HIS 0.006 0.001 HIS B 658 PHE 0.019 0.001 PHE A 12 TYR 0.013 0.001 TYR B 273 ARG 0.003 0.000 ARG D 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8650 (t0) cc_final: 0.8381 (t0) REVERT: A 82 MET cc_start: 0.8984 (mtp) cc_final: 0.8421 (mtm) REVERT: A 94 MET cc_start: 0.8838 (mtp) cc_final: 0.8134 (mtp) REVERT: A 176 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8358 (p0) REVERT: A 440 MET cc_start: 0.9148 (mmm) cc_final: 0.8499 (tpt) REVERT: A 444 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8429 (tm-30) REVERT: A 612 MET cc_start: 0.9311 (OUTLIER) cc_final: 0.9043 (tpp) REVERT: B 661 ASP cc_start: 0.9128 (m-30) cc_final: 0.8783 (m-30) REVERT: C 17 MET cc_start: 0.7845 (mmt) cc_final: 0.7583 (mmm) REVERT: C 29 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8452 (mptt) outliers start: 33 outliers final: 15 residues processed: 142 average time/residue: 0.3350 time to fit residues: 69.7850 Evaluate side-chains 134 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 660 MET Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 0.8980 chunk 93 optimal weight: 0.0000 chunk 2 optimal weight: 0.1980 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 152 GLN ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14473 Z= 0.166 Angle : 0.476 7.000 19561 Z= 0.244 Chirality : 0.039 0.161 2125 Planarity : 0.004 0.036 2526 Dihedral : 3.786 21.183 1891 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.49 % Favored : 96.33 % Rotamer: Outliers : 1.81 % Allowed : 19.42 % Favored : 78.77 % 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 (0.21), residues: 1718 helix: 1.78 (0.17), residues: 966 sheet: 0.24 (0.44), residues: 143 loop : 0.39 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 561 HIS 0.006 0.001 HIS B 658 PHE 0.021 0.001 PHE A 12 TYR 0.012 0.001 TYR B 273 ARG 0.006 0.000 ARG D 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8658 (t0) cc_final: 0.8315 (t0) REVERT: A 82 MET cc_start: 0.9009 (mtp) cc_final: 0.8450 (mtm) REVERT: A 94 MET cc_start: 0.8795 (mtp) cc_final: 0.8059 (mtp) REVERT: A 134 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8631 (m-80) REVERT: A 176 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8123 (p0) REVERT: A 183 MET cc_start: 0.8995 (mtp) cc_final: 0.8235 (mmm) REVERT: A 440 MET cc_start: 0.9146 (mmm) cc_final: 0.8502 (tpt) REVERT: A 444 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8409 (tm-30) REVERT: A 612 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.9064 (tpp) REVERT: B 661 ASP cc_start: 0.9117 (m-30) cc_final: 0.8684 (m-30) REVERT: C 17 MET cc_start: 0.7867 (mmt) cc_final: 0.7589 (mmm) REVERT: C 29 LYS cc_start: 0.8967 (mmmm) cc_final: 0.8442 (mptt) REVERT: C 34 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8343 (tm-30) REVERT: D 24 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8439 (ttp80) outliers start: 28 outliers final: 17 residues processed: 141 average time/residue: 0.2836 time to fit residues: 58.0926 Evaluate side-chains 135 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 660 MET Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 165 optimal weight: 8.9990 chunk 137 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14473 Z= 0.188 Angle : 0.484 6.507 19561 Z= 0.248 Chirality : 0.039 0.147 2125 Planarity : 0.004 0.036 2526 Dihedral : 3.767 21.373 1891 Min Nonbonded Distance : 1.636 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.61 % Favored : 96.22 % Rotamer: Outliers : 1.68 % Allowed : 19.68 % Favored : 78.65 % 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: 1.71 (0.21), residues: 1718 helix: 1.82 (0.17), residues: 966 sheet: 0.29 (0.44), residues: 143 loop : 0.38 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 561 HIS 0.007 0.001 HIS B 658 PHE 0.015 0.001 PHE A 19 TYR 0.012 0.001 TYR B 273 ARG 0.006 0.000 ARG D 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8675 (t0) cc_final: 0.8336 (t0) REVERT: A 82 MET cc_start: 0.9029 (mtp) cc_final: 0.8595 (mtt) REVERT: A 94 MET cc_start: 0.8822 (mtp) cc_final: 0.7964 (mtp) REVERT: A 134 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8659 (m-80) REVERT: A 176 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8403 (m-40) REVERT: A 183 MET cc_start: 0.8999 (mtp) cc_final: 0.8223 (mmm) REVERT: A 440 MET cc_start: 0.9146 (mmm) cc_final: 0.8851 (mmm) REVERT: A 444 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8316 (tm-30) REVERT: A 612 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.9057 (tpp) REVERT: B 72 MET cc_start: 0.9053 (tmm) cc_final: 0.8847 (tmm) REVERT: B 661 ASP cc_start: 0.9136 (m-30) cc_final: 0.8706 (m-30) REVERT: C 17 MET cc_start: 0.7879 (mmt) cc_final: 0.7617 (mmm) REVERT: C 29 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8445 (mptt) REVERT: D 24 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8446 (ttp80) outliers start: 26 outliers final: 17 residues processed: 130 average time/residue: 0.2980 time to fit residues: 57.0391 Evaluate side-chains 133 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 94 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 139 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 164 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14473 Z= 0.172 Angle : 0.480 6.773 19561 Z= 0.245 Chirality : 0.038 0.148 2125 Planarity : 0.004 0.036 2526 Dihedral : 3.746 20.747 1891 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.61 % Favored : 96.22 % Rotamer: Outliers : 1.94 % Allowed : 19.42 % Favored : 78.65 % 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: 1.75 (0.21), residues: 1718 helix: 1.85 (0.17), residues: 967 sheet: 0.32 (0.44), residues: 143 loop : 0.37 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 561 HIS 0.007 0.001 HIS B 658 PHE 0.011 0.001 PHE A 19 TYR 0.012 0.001 TYR B 273 ARG 0.005 0.000 ARG D 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8684 (t0) cc_final: 0.8345 (t0) REVERT: A 82 MET cc_start: 0.9034 (mtp) cc_final: 0.8526 (mtt) REVERT: A 94 MET cc_start: 0.8817 (mtp) cc_final: 0.7935 (mtp) REVERT: A 134 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8655 (m-80) REVERT: A 176 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8247 (m-40) REVERT: A 183 MET cc_start: 0.9056 (mtp) cc_final: 0.8261 (mmm) REVERT: A 440 MET cc_start: 0.9163 (mmm) cc_final: 0.8864 (mmm) REVERT: A 444 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8310 (tm-30) REVERT: A 612 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.9053 (tpp) REVERT: B 72 MET cc_start: 0.9031 (tmm) cc_final: 0.8819 (tmm) REVERT: B 661 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8659 (m-30) REVERT: B 710 MET cc_start: 0.9543 (ttp) cc_final: 0.9340 (ttp) REVERT: C 17 MET cc_start: 0.7868 (mmt) cc_final: 0.7617 (mmm) REVERT: C 29 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8443 (mptt) REVERT: D 24 ARG cc_start: 0.8666 (ttp80) cc_final: 0.8444 (ttp80) outliers start: 30 outliers final: 19 residues processed: 136 average time/residue: 0.2986 time to fit residues: 59.9764 Evaluate side-chains 137 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 152 GLN ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14473 Z= 0.229 Angle : 0.504 7.242 19561 Z= 0.258 Chirality : 0.039 0.147 2125 Planarity : 0.004 0.036 2526 Dihedral : 3.758 21.200 1891 Min Nonbonded Distance : 1.579 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.73 % Favored : 96.10 % Rotamer: Outliers : 1.81 % Allowed : 19.94 % Favored : 78.26 % 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: 1.76 (0.21), residues: 1718 helix: 1.88 (0.17), residues: 967 sheet: 0.27 (0.44), residues: 143 loop : 0.35 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.007 0.001 HIS B 658 PHE 0.013 0.001 PHE B 588 TYR 0.013 0.001 TYR B 273 ARG 0.004 0.000 ARG D 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8694 (t0) cc_final: 0.8347 (t0) REVERT: A 82 MET cc_start: 0.9046 (mtp) cc_final: 0.8557 (mtt) REVERT: A 94 MET cc_start: 0.8840 (mtp) cc_final: 0.7951 (mtp) REVERT: A 176 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8392 (p0) REVERT: A 183 MET cc_start: 0.9066 (mtp) cc_final: 0.8252 (mmm) REVERT: A 440 MET cc_start: 0.9153 (mmm) cc_final: 0.8849 (mmm) REVERT: A 444 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8314 (tm-30) REVERT: A 612 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.9063 (tpp) REVERT: B 661 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8708 (m-30) REVERT: C 17 MET cc_start: 0.7905 (mmt) cc_final: 0.7651 (mmm) REVERT: C 29 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8455 (mptt) REVERT: D 24 ARG cc_start: 0.8663 (ttp80) cc_final: 0.8440 (ttp80) outliers start: 28 outliers final: 19 residues processed: 131 average time/residue: 0.2984 time to fit residues: 57.3543 Evaluate side-chains 135 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 0.5980 chunk 157 optimal weight: 0.8980 chunk 144 optimal weight: 0.0870 chunk 153 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 138 optimal weight: 0.2980 chunk 145 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14473 Z= 0.169 Angle : 0.495 9.558 19561 Z= 0.251 Chirality : 0.038 0.147 2125 Planarity : 0.004 0.037 2526 Dihedral : 3.753 20.563 1891 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.61 % Favored : 96.22 % Rotamer: Outliers : 1.87 % Allowed : 19.87 % Favored : 78.26 % 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: 1.80 (0.21), residues: 1718 helix: 1.94 (0.17), residues: 962 sheet: 0.28 (0.44), residues: 143 loop : 0.32 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 561 HIS 0.007 0.001 HIS B 658 PHE 0.016 0.001 PHE B 588 TYR 0.012 0.001 TYR B 273 ARG 0.004 0.000 ARG D 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8697 (t0) cc_final: 0.8357 (t0) REVERT: A 82 MET cc_start: 0.9034 (mtp) cc_final: 0.8512 (mtt) REVERT: A 94 MET cc_start: 0.8815 (mtp) cc_final: 0.7923 (mtp) REVERT: A 183 MET cc_start: 0.9087 (mtp) cc_final: 0.8160 (mmm) REVERT: A 440 MET cc_start: 0.9138 (mmm) cc_final: 0.8536 (tpt) REVERT: A 444 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8321 (tm-30) REVERT: A 612 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.9056 (tpp) REVERT: B 660 MET cc_start: 0.9446 (ttm) cc_final: 0.9240 (mtm) REVERT: B 661 ASP cc_start: 0.9167 (OUTLIER) cc_final: 0.8718 (m-30) REVERT: C 17 MET cc_start: 0.7894 (mmt) cc_final: 0.7636 (mmm) REVERT: C 34 GLN cc_start: 0.8607 (tm130) cc_final: 0.8349 (tm-30) REVERT: D 24 ARG cc_start: 0.8669 (ttp80) cc_final: 0.8454 (ttp80) outliers start: 29 outliers final: 21 residues processed: 135 average time/residue: 0.3087 time to fit residues: 60.9474 Evaluate side-chains 136 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 0.0470 chunk 99 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 112 optimal weight: 0.9980 chunk 170 optimal weight: 0.4980 chunk 156 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14473 Z= 0.168 Angle : 0.499 9.079 19561 Z= 0.252 Chirality : 0.038 0.148 2125 Planarity : 0.003 0.037 2526 Dihedral : 3.714 20.570 1891 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.43 % Favored : 96.39 % Rotamer: Outliers : 1.68 % Allowed : 20.32 % Favored : 78.00 % 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: 1.86 (0.21), residues: 1718 helix: 1.98 (0.17), residues: 963 sheet: 0.32 (0.44), residues: 143 loop : 0.36 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 561 HIS 0.007 0.001 HIS B 658 PHE 0.016 0.001 PHE B 588 TYR 0.012 0.001 TYR B 273 ARG 0.011 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8657 (t0) cc_final: 0.8313 (t0) REVERT: A 82 MET cc_start: 0.9049 (mtp) cc_final: 0.8518 (mtt) REVERT: A 94 MET cc_start: 0.8829 (mtp) cc_final: 0.7939 (mtp) REVERT: A 183 MET cc_start: 0.9008 (mtp) cc_final: 0.8213 (mmm) REVERT: A 377 GLU cc_start: 0.8773 (mp0) cc_final: 0.8460 (pm20) REVERT: A 415 MET cc_start: 0.9610 (mmm) cc_final: 0.9319 (mmm) REVERT: A 440 MET cc_start: 0.9146 (mmm) cc_final: 0.8843 (mmm) REVERT: A 444 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8315 (tm-30) REVERT: B 661 ASP cc_start: 0.9176 (OUTLIER) cc_final: 0.8713 (m-30) REVERT: C 17 MET cc_start: 0.7888 (mmt) cc_final: 0.7628 (mmm) REVERT: C 29 LYS cc_start: 0.8752 (mmmm) cc_final: 0.8233 (mptt) REVERT: C 34 GLN cc_start: 0.8629 (tm130) cc_final: 0.8375 (tm-30) REVERT: D 24 ARG cc_start: 0.8669 (ttp80) cc_final: 0.8457 (ttp80) outliers start: 26 outliers final: 22 residues processed: 137 average time/residue: 0.2976 time to fit residues: 59.7778 Evaluate side-chains 139 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 661 ASP Chi-restraints excluded: chain B residue 672 TYR 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 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 0.4980 chunk 135 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 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 = 0.3084 r_free = 0.3084 target = 0.050102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.036922 restraints weight = 54869.337| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 3.67 r_work: 0.2498 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14473 Z= 0.244 Angle : 0.530 9.977 19561 Z= 0.267 Chirality : 0.040 0.281 2125 Planarity : 0.004 0.036 2526 Dihedral : 3.773 20.981 1891 Min Nonbonded Distance : 1.569 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 95.98 % Rotamer: Outliers : 1.55 % Allowed : 20.52 % Favored : 77.94 % 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: 1.80 (0.21), residues: 1718 helix: 1.93 (0.17), residues: 968 sheet: 0.32 (0.44), residues: 143 loop : 0.31 (0.27), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 561 HIS 0.008 0.001 HIS B 658 PHE 0.014 0.001 PHE B 588 TYR 0.014 0.001 TYR B 97 ARG 0.003 0.000 ARG C 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2884.24 seconds wall clock time: 53 minutes 34.77 seconds (3214.77 seconds total)