Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 10:07:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhg_24460/04_2023/7rhg_24460_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhg_24460/04_2023/7rhg_24460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhg_24460/04_2023/7rhg_24460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhg_24460/04_2023/7rhg_24460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhg_24460/04_2023/7rhg_24460_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhg_24460/04_2023/7rhg_24460_updated.pdb" } resolution = 2.88 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 82 5.16 5 C 9625 2.51 5 N 2405 2.21 5 O 2637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 14753 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "B" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3542 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 1 Chain: "A" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3717 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain: "D" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3717 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 7.37, per 1000 atoms: 0.50 Number of scatterers: 14753 At special positions: 0 Unit cell: (97.556, 98.397, 119.422, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 4 15.00 O 2637 8.00 N 2405 7.00 C 9625 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: 5.55 Conformation dependent library (CDL) restraints added in 2.1 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3386 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 9 sheets defined 60.7% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'C' and resid 163 through 188 Proline residue: C 175 - end of helix removed outlier: 3.599A pdb=" N VAL C 183 " --> pdb=" O ASN C 179 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 197 through 218 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 268 through 291 removed outlier: 4.193A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG C 277 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER C 279 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 289 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 325 Processing helix chain 'C' and resid 345 through 361 Processing helix chain 'C' and resid 372 through 403 Processing helix chain 'C' and resid 405 through 423 Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 450 through 456 removed outlier: 4.486A pdb=" N TYR C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 476 removed outlier: 6.271A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 493 removed outlier: 3.840A pdb=" N VAL C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 587 removed outlier: 4.653A pdb=" N GLU C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 604 Processing helix chain 'B' and resid 654 through 679 Proline residue: B 675 - end of helix Processing helix chain 'B' and resid 688 through 708 Processing helix chain 'B' and resid 725 through 734 removed outlier: 3.510A pdb=" N LEU B 733 " --> pdb=" O ARG B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 743 Processing helix chain 'B' and resid 759 through 767 Proline residue: B 764 - end of helix Processing helix chain 'B' and resid 770 through 782 removed outlier: 3.785A pdb=" N SER B 781 " --> pdb=" O SER B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 816 Processing helix chain 'B' and resid 833 through 843 Processing helix chain 'B' and resid 855 through 886 Processing helix chain 'B' and resid 888 through 906 Processing helix chain 'B' and resid 911 through 928 removed outlier: 3.565A pdb=" N ARG B 916 " --> pdb=" O SER B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 939 removed outlier: 4.059A pdb=" N VAL B 938 " --> pdb=" O GLU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 959 removed outlier: 6.272A pdb=" N ASN B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 977 Processing helix chain 'B' and resid 1030 through 1034 Processing helix chain 'B' and resid 1059 through 1065 Processing helix chain 'B' and resid 1070 through 1081 Processing helix chain 'A' and resid 163 through 188 removed outlier: 3.570A pdb=" N LEU A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 3.702A pdb=" N VAL A 183 " --> pdb=" O ASN A 179 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 197 through 220 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 257 through 263 removed outlier: 3.550A pdb=" N PHE A 261 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 263 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 291 removed outlier: 4.168A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 277 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 325 Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 372 through 403 Processing helix chain 'A' and resid 405 through 424 Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 459 through 474 removed outlier: 6.110A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 493 Processing helix chain 'A' and resid 578 through 587 removed outlier: 4.859A pdb=" N GLU A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 605 Processing helix chain 'D' and resid 163 through 188 Proline residue: D 175 - end of helix removed outlier: 5.286A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 233 through 241 Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 257 through 263 removed outlier: 3.591A pdb=" N PHE D 261 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU D 263 " --> pdb=" O TYR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 289 removed outlier: 4.248A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 277 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER D 279 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D 282 " --> pdb=" O SER D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 325 Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'D' and resid 372 through 403 Processing helix chain 'D' and resid 405 through 423 Processing helix chain 'D' and resid 428 through 443 Processing helix chain 'D' and resid 450 through 456 removed outlier: 3.883A pdb=" N TYR D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 475 removed outlier: 5.858A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 493 Processing helix chain 'D' and resid 578 through 587 removed outlier: 4.633A pdb=" N GLU D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 605 Processing sheet with id= A, first strand: chain 'C' and resid 496 through 499 Processing sheet with id= B, first strand: chain 'C' and resid 524 through 527 removed outlier: 4.002A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 715 through 717 removed outlier: 3.873A pdb=" N PHE B 715 " --> pdb=" O ILE B 722 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 979 through 983 removed outlier: 6.498A pdb=" N PHE B1055 " --> pdb=" O ILE B1002 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE B1002 " --> pdb=" O PHE B1055 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU B1057 " --> pdb=" O TYR B1000 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR B1000 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 1046 through 1048 removed outlier: 3.783A pdb=" N VAL B1020 " --> pdb=" O VAL B1009 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY B1011 " --> pdb=" O VAL B1018 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL B1018 " --> pdb=" O GLY B1011 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 496 through 500 removed outlier: 6.653A pdb=" N PHE A 574 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE A 519 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 576 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR A 517 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 564 through 567 removed outlier: 3.841A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 536 " --> pdb=" O VAL A 526 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 496 through 500 removed outlier: 6.549A pdb=" N PHE D 574 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE D 519 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU D 576 " --> pdb=" O TYR D 517 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TYR D 517 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 524 through 527 removed outlier: 3.735A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2226 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: 4.51 Time building geometry restraints manager: 6.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4540 1.34 - 1.46: 3203 1.46 - 1.58: 7221 1.58 - 1.69: 9 1.69 - 1.81: 138 Bond restraints: 15111 Sorted by residual: bond pdb=" N PRO B 685 " pdb=" CD PRO B 685 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.13e+01 bond pdb=" CB PRO B 685 " pdb=" CG PRO B 685 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.76e+00 bond pdb=" CB THR B 842 " pdb=" CG2 THR B 842 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.52e+00 bond pdb=" CB VAL A 492 " pdb=" CG1 VAL A 492 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.59e+00 bond pdb=" CB VAL A 350 " pdb=" CG1 VAL A 350 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.75e+00 ... (remaining 15106 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.58: 249 105.58 - 113.25: 8237 113.25 - 120.92: 7718 120.92 - 128.59: 4184 128.59 - 136.26: 105 Bond angle restraints: 20493 Sorted by residual: angle pdb=" C ASN B 830 " pdb=" N SER B 831 " pdb=" CA SER B 831 " ideal model delta sigma weight residual 121.54 127.15 -5.61 1.91e+00 2.74e-01 8.62e+00 angle pdb=" C3' CMP C 701 " pdb=" O3' CMP C 701 " pdb=" P CMP C 701 " ideal model delta sigma weight residual 120.50 111.94 8.56 3.00e+00 1.11e-01 8.14e+00 angle pdb=" C3' CMP A 701 " pdb=" O3' CMP A 701 " pdb=" P CMP A 701 " ideal model delta sigma weight residual 120.50 112.10 8.40 3.00e+00 1.11e-01 7.85e+00 angle pdb=" C3' CMP D 701 " pdb=" O3' CMP D 701 " pdb=" P CMP D 701 " ideal model delta sigma weight residual 120.50 112.35 8.15 3.00e+00 1.11e-01 7.38e+00 angle pdb=" C3' CMP B1301 " pdb=" O3' CMP B1301 " pdb=" P CMP B1301 " ideal model delta sigma weight residual 120.50 112.68 7.82 3.00e+00 1.11e-01 6.80e+00 ... (remaining 20488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.48: 8813 34.48 - 68.96: 118 68.96 - 103.44: 16 103.44 - 137.92: 4 137.92 - 172.39: 8 Dihedral angle restraints: 8959 sinusoidal: 3675 harmonic: 5284 Sorted by residual: dihedral pdb=" C3' CMP C 701 " pdb=" O3' CMP C 701 " pdb=" P CMP C 701 " pdb=" O1P CMP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 112.39 -172.39 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C3' CMP A 701 " pdb=" O3' CMP A 701 " pdb=" P CMP A 701 " pdb=" O1P CMP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 112.38 -172.38 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C3' CMP D 701 " pdb=" O3' CMP D 701 " pdb=" P CMP D 701 " pdb=" O1P CMP D 701 " ideal model delta sinusoidal sigma weight residual -60.00 111.48 -171.48 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 8956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1461 0.033 - 0.067: 593 0.067 - 0.100: 179 0.100 - 0.133: 50 0.133 - 0.166: 6 Chirality restraints: 2289 Sorted by residual: chirality pdb=" CB VAL B 757 " pdb=" CA VAL B 757 " pdb=" CG1 VAL B 757 " pdb=" CG2 VAL B 757 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE A 254 " pdb=" N ILE A 254 " pdb=" C ILE A 254 " pdb=" CB ILE A 254 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA ILE C 254 " pdb=" N ILE C 254 " pdb=" C ILE C 254 " pdb=" CB ILE C 254 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 2286 not shown) Planarity restraints: 2524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 763 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO B 764 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 339 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO D 340 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 340 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 340 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 382 " -0.016 2.00e-02 2.50e+03 1.48e-02 3.81e+00 pdb=" CG PHE A 382 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 382 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 382 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 382 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 382 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 382 " -0.002 2.00e-02 2.50e+03 ... (remaining 2521 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 820 2.74 - 3.28: 15311 3.28 - 3.82: 26866 3.82 - 4.36: 31468 4.36 - 4.90: 52915 Nonbonded interactions: 127380 Sorted by model distance: nonbonded pdb=" O THR C 357 " pdb=" OG1 THR C 361 " model vdw 2.196 2.440 nonbonded pdb=" O LEU C 169 " pdb=" OG1 THR C 173 " model vdw 2.221 2.440 nonbonded pdb=" O LEU D 169 " pdb=" OG1 THR D 173 " model vdw 2.241 2.440 nonbonded pdb=" O THR A 357 " pdb=" OG1 THR A 361 " model vdw 2.269 2.440 nonbonded pdb=" OE2 GLU A 515 " pdb=" OH TYR A 517 " model vdw 2.272 2.440 ... (remaining 127375 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 156 through 605 or resid 701)) selection = chain 'C' selection = (chain 'D' and (resid 156 through 605 or resid 701)) } 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: 1.640 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: 6.610 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 37.420 Find NCS groups from input model: 0.950 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:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 0.097 15111 Z= 0.195 Angle : 0.573 8.561 20493 Z= 0.299 Chirality : 0.041 0.166 2289 Planarity : 0.004 0.065 2524 Dihedral : 15.356 172.395 5573 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 0.00 % 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: 0.74 (0.19), residues: 1780 helix: 0.77 (0.14), residues: 1141 sheet: 0.38 (0.72), residues: 44 loop : 0.20 (0.26), residues: 595 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.650 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 1.3846 time to fit residues: 290.6742 Evaluate side-chains 137 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.783 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 0.0020 chunk 72 optimal weight: 0.1980 chunk 139 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 758 ASN B 805 ASN B 864 ASN B1068 HIS A 411 GLN D 243 ASN D 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 15111 Z= 0.131 Angle : 0.455 9.209 20493 Z= 0.238 Chirality : 0.037 0.152 2289 Planarity : 0.004 0.052 2524 Dihedral : 12.276 163.135 2033 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 1.18 % 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: 1.64 (0.20), residues: 1780 helix: 1.51 (0.15), residues: 1130 sheet: 0.65 (0.66), residues: 50 loop : 0.49 (0.26), residues: 600 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 1.823 Fit side-chains outliers start: 19 outliers final: 6 residues processed: 166 average time/residue: 1.3495 time to fit residues: 246.7745 Evaluate side-chains 142 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 1.844 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.1858 time to fit residues: 3.3515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 144 optimal weight: 0.0070 chunk 160 optimal weight: 0.0770 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 964 GLN B1053 ASN A 411 GLN D 411 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 15111 Z= 0.128 Angle : 0.439 9.073 20493 Z= 0.227 Chirality : 0.037 0.148 2289 Planarity : 0.003 0.043 2524 Dihedral : 12.200 162.293 2033 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 1.06 % 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: 1.99 (0.20), residues: 1780 helix: 1.85 (0.15), residues: 1123 sheet: 0.61 (0.68), residues: 43 loop : 0.51 (0.26), residues: 614 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.673 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 162 average time/residue: 1.2125 time to fit residues: 218.4752 Evaluate side-chains 146 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 1.616 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.1347 time to fit residues: 2.6297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 17 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 143 optimal weight: 0.2980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 GLN A 411 GLN D 243 ASN D 411 GLN D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 15111 Z= 0.189 Angle : 0.468 7.606 20493 Z= 0.244 Chirality : 0.038 0.148 2289 Planarity : 0.003 0.039 2524 Dihedral : 12.249 163.869 2033 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.20), residues: 1780 helix: 1.81 (0.15), residues: 1133 sheet: 0.60 (0.64), residues: 43 loop : 0.51 (0.27), residues: 604 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 1.847 Fit side-chains outliers start: 24 outliers final: 9 residues processed: 160 average time/residue: 1.2512 time to fit residues: 222.1013 Evaluate side-chains 146 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 1.735 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 2.3914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.0470 chunk 2 optimal weight: 0.9980 chunk 128 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 154 optimal weight: 0.4980 chunk 43 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN A 411 GLN D 411 GLN D 559 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 15111 Z= 0.127 Angle : 0.437 6.721 20493 Z= 0.225 Chirality : 0.037 0.149 2289 Planarity : 0.003 0.037 2524 Dihedral : 12.181 162.377 2033 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.20), residues: 1780 helix: 2.00 (0.15), residues: 1127 sheet: 0.65 (0.65), residues: 43 loop : 0.51 (0.26), residues: 610 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 1.801 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 157 average time/residue: 1.3849 time to fit residues: 240.2112 Evaluate side-chains 140 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 1.836 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 2.5858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 172 optimal weight: 0.0470 chunk 142 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1053 ASN A 411 GLN D 411 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 15111 Z= 0.156 Angle : 0.446 6.381 20493 Z= 0.232 Chirality : 0.037 0.146 2289 Planarity : 0.003 0.037 2524 Dihedral : 12.201 162.808 2033 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.20), residues: 1780 helix: 2.04 (0.15), residues: 1127 sheet: 0.66 (0.63), residues: 43 loop : 0.54 (0.27), residues: 610 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.848 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 151 average time/residue: 1.3603 time to fit residues: 226.9246 Evaluate side-chains 140 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 1.879 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 2.6142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 106 optimal weight: 0.5980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN D 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 15111 Z= 0.205 Angle : 0.476 6.517 20493 Z= 0.248 Chirality : 0.038 0.145 2289 Planarity : 0.003 0.038 2524 Dihedral : 12.250 163.832 2033 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.20), residues: 1780 helix: 1.91 (0.15), residues: 1133 sheet: 0.80 (0.63), residues: 43 loop : 0.55 (0.27), residues: 604 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 1.918 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 152 average time/residue: 1.3572 time to fit residues: 227.4804 Evaluate side-chains 142 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.457 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 2.2012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 498 GLN D 411 GLN D 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 15111 Z= 0.157 Angle : 0.452 6.672 20493 Z= 0.234 Chirality : 0.037 0.147 2289 Planarity : 0.003 0.039 2524 Dihedral : 12.210 162.510 2033 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.20), residues: 1780 helix: 1.98 (0.15), residues: 1133 sheet: 0.92 (0.65), residues: 43 loop : 0.59 (0.27), residues: 604 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 1.682 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 150 average time/residue: 1.3653 time to fit residues: 226.5207 Evaluate side-chains 141 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.845 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 1.2511 time to fit residues: 3.8832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 498 GLN D 411 GLN D 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 15111 Z= 0.213 Angle : 0.479 7.418 20493 Z= 0.249 Chirality : 0.038 0.147 2289 Planarity : 0.003 0.039 2524 Dihedral : 12.258 163.699 2033 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.20), residues: 1780 helix: 1.88 (0.15), residues: 1133 sheet: 0.91 (0.65), residues: 43 loop : 0.56 (0.27), residues: 604 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 1.804 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 147 average time/residue: 1.3406 time to fit residues: 217.9761 Evaluate side-chains 143 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 1 average time/residue: 0.1810 time to fit residues: 2.7118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 163 optimal weight: 0.0010 chunk 141 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 498 GLN D 411 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 15111 Z= 0.158 Angle : 0.457 8.993 20493 Z= 0.236 Chirality : 0.038 0.147 2289 Planarity : 0.003 0.040 2524 Dihedral : 12.219 162.586 2033 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.20), residues: 1780 helix: 1.90 (0.15), residues: 1147 sheet: 0.94 (0.65), residues: 43 loop : 0.52 (0.27), residues: 590 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 1.774 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 143 average time/residue: 1.4007 time to fit residues: 220.6179 Evaluate side-chains 143 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 131 time to evaluate : 1.744 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 2 average time/residue: 0.7336 time to fit residues: 3.9556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 39 optimal weight: 0.0030 chunk 141 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.0050 chunk 26 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.0808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN A 498 GLN D 411 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.093133 restraints weight = 18296.698| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.31 r_work: 0.2889 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 15111 Z= 0.170 Angle : 0.461 9.165 20493 Z= 0.239 Chirality : 0.038 0.146 2289 Planarity : 0.003 0.040 2524 Dihedral : 12.226 162.832 2033 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.20), residues: 1780 helix: 1.90 (0.15), residues: 1147 sheet: 0.97 (0.65), residues: 43 loop : 0.53 (0.27), residues: 590 =============================================================================== Job complete usr+sys time: 4426.49 seconds wall clock time: 80 minutes 13.21 seconds (4813.21 seconds total)