Starting phenix.real_space_refine (version: 1.19rc7) on Mon Dec 7 03:58:07 2020 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/12_2020/7jo9_22408.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/12_2020/7jo9_22408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/12_2020/7jo9_22408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/12_2020/7jo9_22408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/12_2020/7jo9_22408.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/12_2020/7jo9_22408.pdb" } resolution = 3.3 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= 0.003 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 14994 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 837 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2961 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1, 'peptide': 358} Link IDs: {'PTRANS': 14, 'TRANS': 342, None: 1, 'PCIS': 1} Not linked: pdbres="ASP K 505 " pdbres=" ZN K 601 " List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13969 SG CYS K 384 40.430 21.150 77.314 1.00 84.47 S ATOM 13975 SG CYS K 385 36.531 21.814 76.213 1.00 87.46 S ATOM 14020 SG CYS K 392 36.749 21.709 79.807 1.00 89.32 S Time building chain proxies: 8.09, per 1000 atoms: 0.54 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Number of scatterers: 14994 At special positions: 0 Unit cell: (121.03, 135.59, 125.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 25 16.00 P 290 15.00 O 3351 8.00 N 2771 7.00 C 8556 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 Amimo 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: 7.17 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 384 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 385 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 392 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 378 " Number of angles added : 3 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 63.0% alpha, 7.4% beta 138 base pairs and 252 stacking pairs defined. Time for finding SS restraints: 6.06 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.512A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.530A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.527A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.670A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.219A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.500A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.610A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 4.043A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.739A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.629A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.703A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 removed outlier: 4.109A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.977A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.596A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.611A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.575A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.102A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.583A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.611A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 4.043A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.739A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.629A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.703A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 4.109A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 185 removed outlier: 4.019A pdb=" N ARG K 161 " --> pdb=" O LEU K 157 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LYS K 162 " --> pdb=" O ARG K 158 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP K 163 " --> pdb=" O LEU K 159 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE K 164 " --> pdb=" O LYS K 160 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ALA K 167 " --> pdb=" O ASP K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 250 No H-bonds generated for 'chain 'K' and resid 248 through 250' Processing helix chain 'K' and resid 258 through 276 removed outlier: 3.741A pdb=" N GLU K 276 " --> pdb=" O GLU K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 319 through 325 removed outlier: 4.400A pdb=" N GLU K 324 " --> pdb=" O SER K 321 " (cutoff:3.500A) Processing helix chain 'K' and resid 333 through 342 removed outlier: 3.535A pdb=" N ARG K 337 " --> pdb=" O GLY K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 377 Processing helix chain 'K' and resid 393 through 412 Processing helix chain 'K' and resid 413 through 416 Processing helix chain 'K' and resid 419 through 434 removed outlier: 3.999A pdb=" N VAL K 423 " --> pdb=" O CYS K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 443 removed outlier: 4.028A pdb=" N ASP K 441 " --> pdb=" O SER K 438 " (cutoff:3.500A) Proline residue: K 442 - end of helix Processing helix chain 'K' and resid 444 through 463 Processing helix chain 'K' and resid 482 through 499 Processing helix chain 'K' and resid 501 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.137A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.629A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.957A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.489A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.767A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 193 through 195 removed outlier: 4.619A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP K 281 " --> pdb=" O ARG K 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 193 through 195 removed outlier: 4.619A pdb=" N MET K 215 " --> pdb=" O LEU K 195 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE K 212 " --> pdb=" O ASP K 307 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE K 309 " --> pdb=" O PHE K 212 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL K 214 " --> pdb=" O ILE K 309 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA K 311 " --> pdb=" O VAL K 214 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N PHE K 216 " --> pdb=" O ALA K 311 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU K 313 " --> pdb=" O PHE K 216 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU K 218 " --> pdb=" O GLU K 313 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU K 310 " --> pdb=" O PRO K 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 223 through 227 Processing sheet with id=AB3, first strand: chain 'K' and resid 252 through 253 511 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 252 stacking parallelities Total time for adding SS restraints: 7.78 Time building geometry restraints manager: 7.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3006 1.33 - 1.45: 4768 1.45 - 1.57: 7469 1.57 - 1.69: 578 1.69 - 1.81: 40 Bond restraints: 15861 Sorted by residual: bond pdb=" C LEU D 102 " pdb=" N PRO D 103 " ideal model delta sigma weight residual 1.334 1.317 0.016 1.11e-02 8.12e+03 2.19e+00 bond pdb=" C LEU H 102 " pdb=" N PRO H 103 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.11e-02 8.12e+03 1.91e+00 bond pdb=" CB LEU D 80 " pdb=" CG LEU D 80 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.59e+00 bond pdb=" CB LEU H 80 " pdb=" CG LEU H 80 " ideal model delta sigma weight residual 1.530 1.505 0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.49e+00 ... (remaining 15856 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.28: 1365 105.28 - 112.46: 8823 112.46 - 119.64: 5238 119.64 - 126.82: 6394 126.82 - 134.00: 814 Bond angle restraints: 22634 Sorted by residual: angle pdb=" CA GLY H 53 " pdb=" C GLY H 53 " pdb=" N ILE H 54 " ideal model delta sigma weight residual 115.27 117.77 -2.50 7.60e-01 1.73e+00 1.08e+01 angle pdb=" CA GLY D 53 " pdb=" C GLY D 53 " pdb=" N ILE D 54 " ideal model delta sigma weight residual 115.27 117.71 -2.44 7.60e-01 1.73e+00 1.03e+01 angle pdb=" N ARG K 222 " pdb=" CA ARG K 222 " pdb=" C ARG K 222 " ideal model delta sigma weight residual 111.02 114.33 -3.31 1.25e+00 6.40e-01 7.00e+00 angle pdb=" CB MET F 84 " pdb=" CG MET F 84 " pdb=" SD MET F 84 " ideal model delta sigma weight residual 112.70 104.77 7.93 3.00e+00 1.11e-01 6.99e+00 angle pdb=" C ARG D 33 " pdb=" CA ARG D 33 " pdb=" CB ARG D 33 " ideal model delta sigma weight residual 109.80 114.06 -4.26 1.70e+00 3.46e-01 6.29e+00 ... (remaining 22629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.52: 7097 33.52 - 67.04: 1453 67.04 - 100.56: 40 100.56 - 134.08: 0 134.08 - 167.60: 1 Dihedral angle restraints: 8591 sinusoidal: 5316 harmonic: 3275 Sorted by residual: dihedral pdb=" CA ARG H 33 " pdb=" C ARG H 33 " pdb=" N LYS H 34 " pdb=" CA LYS H 34 " ideal model delta harmonic sigma weight residual -180.00 -155.78 -24.22 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA ARG D 33 " pdb=" C ARG D 33 " pdb=" N LYS D 34 " pdb=" CA LYS D 34 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 52.40 167.60 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 8588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1386 0.029 - 0.059: 777 0.059 - 0.088: 279 0.088 - 0.117: 80 0.117 - 0.147: 25 Chirality restraints: 2547 Sorted by residual: chirality pdb=" CB ILE H 54 " pdb=" CA ILE H 54 " pdb=" CG1 ILE H 54 " pdb=" CG2 ILE H 54 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA PRO H 50 " pdb=" N PRO H 50 " pdb=" C PRO H 50 " pdb=" CB PRO H 50 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 2544 not shown) Planarity restraints: 1861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER K 446 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C SER K 446 " -0.055 2.00e-02 2.50e+03 pdb=" O SER K 446 " 0.020 2.00e-02 2.50e+03 pdb=" N SER K 447 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 454 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C ALA K 454 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA K 454 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE K 455 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER K 447 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C SER K 447 " 0.051 2.00e-02 2.50e+03 pdb=" O SER K 447 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS K 448 " -0.017 2.00e-02 2.50e+03 ... (remaining 1858 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2251 2.76 - 3.29: 13369 3.29 - 3.83: 26368 3.83 - 4.36: 30229 4.36 - 4.90: 45966 Nonbonded interactions: 118183 Sorted by model distance: nonbonded pdb=" OE1 GLU C 64 " pdb=" NH2 ARG K 222 " model vdw 2.222 2.520 nonbonded pdb=" OH TYR K 421 " pdb=" NE2 HIS K 467 " model vdw 2.237 2.520 nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG K 241 " model vdw 2.255 2.520 nonbonded pdb=" NH2 ARG F 19 " pdb=" OP1 DA J -22 " model vdw 2.276 2.520 nonbonded pdb=" O ARG E 129 " pdb=" NH1 ARG E 129 " model vdw 2.289 2.520 ... (remaining 118178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 3146 14994 True True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 290 5.49 5 S 25 5.16 5 C 8556 2.51 5 N 2771 2.21 5 O 3351 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 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: 1.880 Set model interpretation parameters: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.870 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.070 Process input model: 53.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.340 Internal consistency checks: 0.000 Total: 66.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.008 0.047 15861 Angle : 0.741 9.645 22634 Chirality : 0.042 0.147 2547 Planarity : 0.005 0.067 1861 Dihedral : 25.999 167.599 6473 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.34 (0.25), residues: 1107 helix: 1.48 (0.20), residues: 646 sheet: -0.28 (0.64), residues: 57 loop : -1.83 (0.28), residues: 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 4 poor density : 231 time to evaluate : 1.295 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 232 average time/residue: 0.4170 time to fit residues: 98.8188 Evaluate side-chains 136 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.395 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN E 68 GLN G 38 ASN K 339 ASN K 429 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.047 15861 Angle : 0.536 6.945 22634 Chirality : 0.034 0.164 2547 Planarity : 0.004 0.053 1861 Dihedral : 29.104 173.117 4159 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.26), residues: 1107 helix: 2.54 (0.21), residues: 661 sheet: 0.36 (0.67), residues: 59 loop : -1.36 (0.30), residues: 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.434 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.3907 time to fit residues: 65.5047 Evaluate side-chains 118 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.692 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 122 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 109 optimal weight: 0.1980 chunk 121 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.069 15861 Angle : 0.524 6.291 22634 Chirality : 0.034 0.127 2547 Planarity : 0.004 0.046 1861 Dihedral : 29.100 175.179 4159 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.94 (0.26), residues: 1107 helix: 2.63 (0.20), residues: 666 sheet: 1.15 (0.72), residues: 54 loop : -1.21 (0.29), residues: 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.419 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.3870 time to fit residues: 57.4574 Evaluate side-chains 111 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN D 63 ASN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.079 15861 Angle : 0.571 5.413 22634 Chirality : 0.036 0.146 2547 Planarity : 0.004 0.054 1861 Dihedral : 29.239 175.662 4159 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.72 (0.25), residues: 1107 helix: 2.44 (0.20), residues: 666 sheet: 0.55 (0.69), residues: 61 loop : -1.20 (0.29), residues: 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.335 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.3979 time to fit residues: 58.7341 Evaluate side-chains 118 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS D 63 ASN E 76 GLN H 47 GLN H 63 ASN K 413 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.008 0.080 15861 Angle : 0.710 8.328 22634 Chirality : 0.044 0.177 2547 Planarity : 0.006 0.053 1861 Dihedral : 29.699 175.386 4159 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.06 (0.25), residues: 1107 helix: 1.86 (0.20), residues: 666 sheet: 1.20 (0.69), residues: 50 loop : -1.48 (0.28), residues: 391 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.377 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.3966 time to fit residues: 56.4736 Evaluate side-chains 120 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.368 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 130 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.058 15861 Angle : 0.518 6.268 22634 Chirality : 0.034 0.131 2547 Planarity : 0.004 0.068 1861 Dihedral : 29.154 174.448 4159 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.25), residues: 1107 helix: 2.50 (0.20), residues: 667 sheet: 1.32 (0.70), residues: 50 loop : -1.20 (0.29), residues: 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.398 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.3837 time to fit residues: 57.8640 Evaluate side-chains 120 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.341 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 0.0970 chunk 80 optimal weight: 4.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.050 15861 Angle : 0.584 5.942 22634 Chirality : 0.037 0.138 2547 Planarity : 0.005 0.059 1861 Dihedral : 29.288 175.306 4159 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 (0.25), residues: 1107 helix: 2.36 (0.20), residues: 666 sheet: 1.28 (0.71), residues: 50 loop : -1.29 (0.28), residues: 391 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.404 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3908 time to fit residues: 54.6693 Evaluate side-chains 120 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS D 63 ASN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.047 15861 Angle : 0.561 10.468 22634 Chirality : 0.035 0.132 2547 Planarity : 0.004 0.067 1861 Dihedral : 29.242 175.339 4159 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.25), residues: 1107 helix: 2.50 (0.20), residues: 667 sheet: 1.33 (0.72), residues: 50 loop : -1.23 (0.28), residues: 390 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.371 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3834 time to fit residues: 52.0153 Evaluate side-chains 120 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.328 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.4980 chunk 121 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.044 15861 Angle : 0.550 8.962 22634 Chirality : 0.035 0.130 2547 Planarity : 0.004 0.061 1861 Dihedral : 29.166 175.305 4159 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.89 (0.25), residues: 1107 helix: 2.56 (0.20), residues: 667 sheet: 1.36 (0.71), residues: 50 loop : -1.20 (0.28), residues: 390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.328 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3677 time to fit residues: 49.9384 Evaluate side-chains 118 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.373 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 chunk 107 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS D 63 ASN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.044 15861 Angle : 0.574 8.571 22634 Chirality : 0.036 0.137 2547 Planarity : 0.004 0.056 1861 Dihedral : 29.195 175.272 4159 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.25), residues: 1107 helix: 2.44 (0.20), residues: 667 sheet: 1.35 (0.70), residues: 50 loop : -1.24 (0.28), residues: 390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield and 0 Emsley and 1107 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 129 time to evaluate : 1.344 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.3826 time to fit residues: 51.5494 Evaluate side-chains 117 residues out of total 969 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.420 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 110 optimal weight: 0.0000 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.158632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.123803 restraints weight = 22138.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123140 restraints weight = 39707.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123161 restraints weight = 35102.141| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.004 0.043 15861 ANGLE : 0.558 8.167 22634 CHIRALITY : 0.035 0.135 2547 PLANARITY : 0.004 0.055 1861 DIHEDRAL : 29.189 175.303 4159 MIN NONBONDED DISTANCE : 2.224 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 4.91 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 2.71 % FAVORED : 97.29 % ROTAMER OUTLIERS : 0.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 2.63 % 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: 1.79 (0.25), RESIDUES: 1107 HELIX: 2.47 (0.20), RESIDUES: 667 SHEET: 1.38 (0.70), RESIDUES: 50 LOOP : -1.24 (0.28), RESIDUES: 390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.043 15861 Angle : 0.558 8.167 22634 Chirality : 0.035 0.135 2547 Planarity : 0.004 0.055 1861 Dihedral : 29.189 175.303 4159 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.79 (0.25), residues: 1107 helix: 2.47 (0.20), residues: 667 sheet: 1.38 (0.70), residues: 50 loop : -1.24 (0.28), residues: 390 =============================================================================== Job complete usr+sys time: 2308.07 seconds wall clock time: 42 minutes 45.39 seconds (2565.39 seconds total)