Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 18:45:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd4_27334/04_2023/8dd4_27334.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd4_27334/04_2023/8dd4_27334.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd4_27334/04_2023/8dd4_27334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd4_27334/04_2023/8dd4_27334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd4_27334/04_2023/8dd4_27334.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd4_27334/04_2023/8dd4_27334.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 6624 2.51 5 N 1807 2.21 5 O 1922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10426 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8076 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 981, 8043 Classifications: {'peptide': 981} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 935} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 981, 8043 Classifications: {'peptide': 981} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 935} Chain breaks: 4 bond proxies already assigned to first conformer: 8187 Chain: "B" Number of atoms: 2329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2329 Classifications: {'peptide': 274} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 269} Chain breaks: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 617 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 617 " occ=0.50 residue: pdb=" N AARG A 651 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 651 " occ=0.50 residue: pdb=" N AARG A 704 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 704 " occ=0.50 Time building chain proxies: 9.25, per 1000 atoms: 0.89 Number of scatterers: 10426 At special positions: 0 Unit cell: (106.029, 132.804, 112.455, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 1922 8.00 N 1807 7.00 C 6624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.10 Conformation dependent library (CDL) restraints added in 3.8 seconds 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 51.7% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.509A pdb=" N GLU A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG A 54 " --> pdb=" O PHE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 108 through 122 Processing helix chain 'A' and resid 124 through 130 removed outlier: 4.024A pdb=" N PHE A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 155 removed outlier: 3.515A pdb=" N GLN A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 removed outlier: 3.571A pdb=" N ALA A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.540A pdb=" N TYR A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 178 through 183' Processing helix chain 'A' and resid 216 through 229 removed outlier: 3.589A pdb=" N THR A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.733A pdb=" N ARG A 309 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.739A pdb=" N VAL A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 330 " --> pdb=" O LEU A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 330' Processing helix chain 'A' and resid 488 through 496 removed outlier: 3.569A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 537 removed outlier: 3.569A pdb=" N ARG A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 557 through 563 removed outlier: 3.886A pdb=" N THR A 560 " --> pdb=" O TYR A 557 " (cutoff:3.500A) Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 564 through 572 removed outlier: 3.521A pdb=" N VAL A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 589 removed outlier: 3.632A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 600 removed outlier: 3.918A pdb=" N GLU A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 603 No H-bonds generated for 'chain 'A' and resid 601 through 603' Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 647 through 658 Processing helix chain 'A' and resid 660 through 674 removed outlier: 3.523A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 696 removed outlier: 3.782A pdb=" N LEU A 687 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY A 696 " --> pdb=" O CYS A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 721 removed outlier: 4.072A pdb=" N LEU A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 739 removed outlier: 3.521A pdb=" N GLN A 731 " --> pdb=" O THR A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 748 removed outlier: 3.992A pdb=" N MET A 745 " --> pdb=" O ARG A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 857 through 865 Processing helix chain 'A' and resid 875 through 885 removed outlier: 3.859A pdb=" N ASN A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 912 Processing helix chain 'A' and resid 940 through 944 removed outlier: 4.237A pdb=" N LYS A 944 " --> pdb=" O LYS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 965 removed outlier: 3.674A pdb=" N VAL A 963 " --> pdb=" O ASP A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 994 removed outlier: 4.529A pdb=" N GLU A 978 " --> pdb=" O THR A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1005 removed outlier: 4.143A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1009 removed outlier: 4.165A pdb=" N GLY A1009 " --> pdb=" O LEU A1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1006 through 1009' Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 4.047A pdb=" N ILE A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A1021 " --> pdb=" O ASP A1017 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A1022 " --> pdb=" O ASP A1018 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A1026 " --> pdb=" O ILE A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1046 removed outlier: 3.989A pdb=" N LEU A1036 " --> pdb=" O GLU A1032 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A1037 " --> pdb=" O GLN A1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.884A pdb=" N GLY B 388 " --> pdb=" O HIS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 410 removed outlier: 3.837A pdb=" N LEU B 404 " --> pdb=" O SER B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 437 removed outlier: 3.545A pdb=" N VAL B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 504 Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.615A pdb=" N PHE B 512 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 588 removed outlier: 3.525A pdb=" N ILE B 521 " --> pdb=" O ASN B 517 " (cutoff:3.500A) Proline residue: B 568 - end of helix Processing helix chain 'B' and resid 591 through 596 removed outlier: 4.011A pdb=" N GLU B 596 " --> pdb=" O LYS B 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 36 removed outlier: 3.719A pdb=" N VAL A 32 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 34 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 20 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 99 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 101 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 102 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 206 through 212 removed outlier: 3.584A pdb=" N TYR A 207 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 340 removed outlier: 4.647A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 385 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.523A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.523A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 402 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASN A 426 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU A 404 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TRP A 424 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 418 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 439 through 444 removed outlier: 3.767A pdb=" N GLY A 439 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET A 441 " --> pdb=" O LEU A 475 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 751 through 752 removed outlier: 3.733A pdb=" N PHE A 751 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 779 through 784 Processing sheet with id=AA9, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AB1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.106A pdb=" N THR B 354 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1416 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: 3.62 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3414 1.34 - 1.46: 2343 1.46 - 1.58: 4756 1.58 - 1.70: 0 1.70 - 1.82: 114 Bond restraints: 10627 Sorted by residual: bond pdb=" CG1 ILE A 819 " pdb=" CD1 ILE A 819 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.66e+00 bond pdb=" C SER A 199 " pdb=" N PRO A 200 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.57e+00 bond pdb=" CA ASP B 337 " pdb=" CB ASP B 337 " ideal model delta sigma weight residual 1.524 1.541 -0.016 1.53e-02 4.27e+03 1.14e+00 bond pdb=" CG LEU A 688 " pdb=" CD1 LEU A 688 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CB LYS A 179 " pdb=" CG LYS A 179 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.29e-01 ... (remaining 10622 not shown) Histogram of bond angle deviations from ideal: 97.09 - 104.47: 154 104.47 - 111.85: 4905 111.85 - 119.24: 3806 119.24 - 126.62: 5301 126.62 - 134.00: 162 Bond angle restraints: 14328 Sorted by residual: angle pdb=" C THR A1052 " pdb=" N THR A1053 " pdb=" CA THR A1053 " ideal model delta sigma weight residual 121.54 128.42 -6.88 1.91e+00 2.74e-01 1.30e+01 angle pdb=" CB MET A 732 " pdb=" CG MET A 732 " pdb=" SD MET A 732 " ideal model delta sigma weight residual 112.70 122.65 -9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" N MET B 525 " pdb=" CA MET B 525 " pdb=" CB MET B 525 " ideal model delta sigma weight residual 110.12 114.72 -4.60 1.47e+00 4.63e-01 9.78e+00 angle pdb=" CB MET A1040 " pdb=" CG MET A1040 " pdb=" SD MET A1040 " ideal model delta sigma weight residual 112.70 121.87 -9.17 3.00e+00 1.11e-01 9.33e+00 angle pdb=" CB LYS B 480 " pdb=" CG LYS B 480 " pdb=" CD LYS B 480 " ideal model delta sigma weight residual 111.30 118.10 -6.80 2.30e+00 1.89e-01 8.75e+00 ... (remaining 14323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5770 17.98 - 35.97: 594 35.97 - 53.95: 113 53.95 - 71.93: 17 71.93 - 89.91: 12 Dihedral angle restraints: 6506 sinusoidal: 2790 harmonic: 3716 Sorted by residual: dihedral pdb=" CA LYS A 573 " pdb=" C LYS A 573 " pdb=" N TRP A 574 " pdb=" CA TRP A 574 " ideal model delta harmonic sigma weight residual 180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA MET B 326 " pdb=" C MET B 326 " pdb=" N SER B 327 " pdb=" CA SER B 327 " ideal model delta harmonic sigma weight residual -180.00 -162.65 -17.35 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP A 646 " pdb=" CB ASP A 646 " pdb=" CG ASP A 646 " pdb=" OD1 ASP A 646 " ideal model delta sinusoidal sigma weight residual -30.00 -88.23 58.23 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 6503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 967 0.033 - 0.067: 404 0.067 - 0.100: 113 0.100 - 0.134: 51 0.134 - 0.167: 7 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA LYS B 480 " pdb=" N LYS B 480 " pdb=" C LYS B 480 " pdb=" CB LYS B 480 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA GLN A 738 " pdb=" N GLN A 738 " pdb=" C GLN A 738 " pdb=" CB GLN A 738 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA THR A1053 " pdb=" N THR A1053 " pdb=" C THR A1053 " pdb=" CB THR A1053 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1539 not shown) Planarity restraints: 1841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 216 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO A 217 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 177 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO A 178 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 56 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO A 57 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.024 5.00e-02 4.00e+02 ... (remaining 1838 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1416 2.76 - 3.29: 10300 3.29 - 3.83: 17329 3.83 - 4.36: 20116 4.36 - 4.90: 34360 Nonbonded interactions: 83521 Sorted by model distance: nonbonded pdb=" O LEU A 540 " pdb=" NH2 ARG B 340 " model vdw 2.219 2.520 nonbonded pdb=" OE2 GLU A 469 " pdb=" NH1 ARG B 481 " model vdw 2.227 2.520 nonbonded pdb=" OH TYR A 584 " pdb=" OD1 ASP A 608 " model vdw 2.237 2.440 nonbonded pdb=" OD1 ASP B 540 " pdb=" NH2 ARG B 543 " model vdw 2.253 2.520 nonbonded pdb=" NZ LYS A 440 " pdb=" OE1 GLU A 474 " model vdw 2.272 2.520 ... (remaining 83516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.350 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: 0.020 Extract box with map and model: 4.300 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 40.760 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 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 0.050 10627 Z= 0.187 Angle : 0.647 9.949 14328 Z= 0.321 Chirality : 0.043 0.167 1542 Planarity : 0.004 0.061 1841 Dihedral : 14.944 89.912 4096 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.82 % Favored : 97.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.24), residues: 1250 helix: 0.84 (0.22), residues: 579 sheet: -0.23 (0.44), residues: 143 loop : -0.42 (0.27), residues: 528 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2458 time to fit residues: 83.7540 Evaluate side-chains 200 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.301 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 370 ASN A 457 ASN ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 10627 Z= 0.342 Angle : 0.674 8.257 14328 Z= 0.347 Chirality : 0.046 0.159 1542 Planarity : 0.005 0.054 1841 Dihedral : 4.202 19.005 1385 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.38 % Favored : 96.45 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1250 helix: 0.78 (0.21), residues: 590 sheet: -0.88 (0.43), residues: 141 loop : -0.45 (0.28), residues: 519 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 194 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 207 average time/residue: 0.2457 time to fit residues: 71.1377 Evaluate side-chains 192 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 177 time to evaluate : 1.335 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0960 time to fit residues: 4.6063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10627 Z= 0.176 Angle : 0.582 13.213 14328 Z= 0.294 Chirality : 0.042 0.156 1542 Planarity : 0.004 0.055 1841 Dihedral : 3.982 17.041 1385 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.82 % Favored : 97.02 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1250 helix: 1.00 (0.21), residues: 589 sheet: -0.94 (0.42), residues: 141 loop : -0.31 (0.28), residues: 520 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 201 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 202 average time/residue: 0.2365 time to fit residues: 67.6825 Evaluate side-chains 186 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0982 time to fit residues: 2.2832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 76 optimal weight: 0.0870 chunk 114 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 overall best weight: 0.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10627 Z= 0.182 Angle : 0.577 10.966 14328 Z= 0.293 Chirality : 0.042 0.157 1542 Planarity : 0.004 0.054 1841 Dihedral : 3.902 17.057 1385 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.22 % Favored : 96.62 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1250 helix: 1.06 (0.21), residues: 592 sheet: -1.00 (0.42), residues: 146 loop : -0.32 (0.28), residues: 512 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 201 average time/residue: 0.2340 time to fit residues: 66.9942 Evaluate side-chains 198 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 185 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0994 time to fit residues: 4.1050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 103 optimal weight: 5.9990 chunk 83 optimal weight: 0.0980 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 GLN ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 10627 Z= 0.157 Angle : 0.554 7.983 14328 Z= 0.282 Chirality : 0.041 0.159 1542 Planarity : 0.003 0.053 1841 Dihedral : 3.826 16.351 1385 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.82 % Favored : 97.02 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1250 helix: 1.15 (0.22), residues: 598 sheet: -0.90 (0.42), residues: 146 loop : -0.30 (0.28), residues: 506 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 199 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 203 average time/residue: 0.2235 time to fit residues: 64.6589 Evaluate side-chains 188 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 183 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1140 time to fit residues: 2.8141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 116 optimal weight: 0.2980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10627 Z= 0.194 Angle : 0.595 15.136 14328 Z= 0.299 Chirality : 0.042 0.189 1542 Planarity : 0.004 0.052 1841 Dihedral : 3.851 16.833 1385 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.90 % Favored : 96.94 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.24), residues: 1250 helix: 1.07 (0.21), residues: 598 sheet: -0.90 (0.42), residues: 146 loop : -0.30 (0.28), residues: 506 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 188 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 193 average time/residue: 0.2360 time to fit residues: 64.8743 Evaluate side-chains 195 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 186 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1048 time to fit residues: 3.5999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 73 optimal weight: 0.2980 chunk 55 optimal weight: 0.0070 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 10627 Z= 0.164 Angle : 0.581 10.481 14328 Z= 0.293 Chirality : 0.042 0.216 1542 Planarity : 0.003 0.052 1841 Dihedral : 3.856 16.444 1385 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.74 % Favored : 97.10 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.24), residues: 1250 helix: 1.09 (0.21), residues: 599 sheet: -0.78 (0.43), residues: 140 loop : -0.24 (0.28), residues: 511 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 198 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 202 average time/residue: 0.2377 time to fit residues: 68.0323 Evaluate side-chains 196 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 191 time to evaluate : 1.270 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0959 time to fit residues: 2.6369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.0020 chunk 94 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 HIS ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 GLN ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10627 Z= 0.175 Angle : 0.603 9.332 14328 Z= 0.303 Chirality : 0.042 0.195 1542 Planarity : 0.004 0.052 1841 Dihedral : 3.901 17.223 1385 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.74 % Favored : 97.10 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1250 helix: 1.12 (0.21), residues: 599 sheet: -0.80 (0.42), residues: 146 loop : -0.31 (0.28), residues: 505 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 202 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 205 average time/residue: 0.2420 time to fit residues: 70.9366 Evaluate side-chains 195 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1148 time to fit residues: 2.8834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 101 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 10627 Z= 0.215 Angle : 0.632 10.684 14328 Z= 0.318 Chirality : 0.043 0.207 1542 Planarity : 0.004 0.052 1841 Dihedral : 4.094 27.906 1385 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.30 % Favored : 96.54 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1250 helix: 1.00 (0.21), residues: 605 sheet: -0.82 (0.44), residues: 138 loop : -0.36 (0.28), residues: 507 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 191 average time/residue: 0.2287 time to fit residues: 62.6254 Evaluate side-chains 190 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1108 time to fit residues: 2.2791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 chunk 78 optimal weight: 0.1980 chunk 105 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10627 Z= 0.186 Angle : 0.623 9.286 14328 Z= 0.314 Chirality : 0.043 0.203 1542 Planarity : 0.004 0.052 1841 Dihedral : 4.091 26.746 1385 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.06 % Favored : 96.78 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1250 helix: 1.03 (0.21), residues: 605 sheet: -0.82 (0.44), residues: 138 loop : -0.34 (0.28), residues: 507 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 191 average time/residue: 0.2325 time to fit residues: 64.6915 Evaluate side-chains 188 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 1.257 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1019 time to fit residues: 2.1728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 41 optimal weight: 0.2980 chunk 101 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.0050 chunk 87 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 ASN ** 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 = 0.4358 r_free = 0.4358 target = 0.183673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.131967 restraints weight = 41448.196| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 4.92 r_work: 0.3464 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 10627 Z= 0.160 Angle : 0.606 9.367 14328 Z= 0.303 Chirality : 0.042 0.200 1542 Planarity : 0.003 0.052 1841 Dihedral : 3.979 26.434 1385 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.22 % Favored : 96.62 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.24), residues: 1250 helix: 1.19 (0.21), residues: 599 sheet: -0.76 (0.43), residues: 144 loop : -0.26 (0.28), residues: 507 =============================================================================== Job complete usr+sys time: 2527.34 seconds wall clock time: 46 minutes 46.25 seconds (2806.25 seconds total)