Starting phenix.real_space_refine on Fri Sep 27 01:11:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/09_2024/7jo9_22408.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/09_2024/7jo9_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_22408/09_2024/7jo9_22408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/09_2024/7jo9_22408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/09_2024/7jo9_22408.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jo9_22408/09_2024/7jo9_22408.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 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. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14994 Number of models: 1 Model: "" Number of chains: 12 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: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2960 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 342} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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: 9.28, per 1000 atoms: 0.62 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 - 3.00 Amino acid : True - 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: 3.38 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 385 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 378 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 392 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 384 " Number of angles added : 3 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. 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: 6.17 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: 6.73 Time building geometry restraints manager: 3.99 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: 0.00 - 1.59: 21551 1.59 - 3.17: 985 3.17 - 4.76: 69 4.76 - 6.35: 21 6.35 - 7.93: 8 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: 7314 33.52 - 67.04: 1488 67.04 - 100.56: 40 100.56 - 134.08: 0 134.08 - 167.60: 1 Dihedral angle restraints: 8843 sinusoidal: 5568 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 8840 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 3.120 nonbonded pdb=" OH TYR K 421 " pdb=" NE2 HIS K 467 " model vdw 2.237 3.120 nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG K 241 " model vdw 2.255 3.120 nonbonded pdb=" NH2 ARG F 19 " pdb=" OP1 DA J -22 " model vdw 2.276 3.120 nonbonded pdb=" O ARG E 129 " pdb=" NH1 ARG E 129 " model vdw 2.289 3.120 ... (remaining 118178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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' } 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: 13.510 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 41.770 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.008 0.047 15861 Z= 0.466 Angle : 0.738 7.933 22634 Z= 0.442 Chirality : 0.042 0.147 2547 Planarity : 0.005 0.067 1861 Dihedral : 25.947 167.599 6725 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.41 % Allowed : 0.72 % Favored : 98.86 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 363 HIS 0.004 0.001 HIS E 39 PHE 0.023 0.002 PHE K 266 TYR 0.023 0.002 TYR K 346 ARG 0.010 0.001 ARG K 443 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 1.199 Fit side-chains REVERT: D 68 ASP cc_start: 0.8115 (t0) cc_final: 0.7913 (t0) REVERT: E 73 GLU cc_start: 0.8100 (tt0) cc_final: 0.7667 (tt0) REVERT: E 90 MET cc_start: 0.7432 (mmp) cc_final: 0.7134 (mmm) REVERT: F 68 ASP cc_start: 0.7764 (m-30) cc_final: 0.7555 (m-30) REVERT: F 91 LYS cc_start: 0.8420 (ttmt) cc_final: 0.8156 (ttmm) REVERT: G 99 LYS cc_start: 0.8417 (mmtm) cc_final: 0.8073 (mmtt) REVERT: K 173 LYS cc_start: 0.5271 (mtmm) cc_final: 0.5067 (mtmt) REVERT: K 269 ILE cc_start: 0.6058 (mt) cc_final: 0.5368 (tt) outliers start: 4 outliers final: 0 residues processed: 232 average time/residue: 0.3946 time to fit residues: 119.2968 Evaluate side-chains 134 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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: 4.9990 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 68 GLN F 25 ASN G 38 ASN H 47 GLN K 339 ASN K 429 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15861 Z= 0.185 Angle : 0.561 6.332 22634 Z= 0.329 Chirality : 0.035 0.126 2547 Planarity : 0.004 0.055 1861 Dihedral : 28.593 171.903 4411 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.55 % Allowed : 8.46 % Favored : 89.99 % 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: 1.69 (0.26), residues: 1107 helix: 2.49 (0.21), residues: 661 sheet: 0.31 (0.65), residues: 58 loop : -1.27 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 363 HIS 0.004 0.001 HIS A 39 PHE 0.014 0.002 PHE K 266 TYR 0.015 0.002 TYR K 373 ARG 0.006 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.318 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8260 (mtpt) REVERT: D 33 ARG cc_start: 0.7027 (ppt170) cc_final: 0.6743 (ptt180) REVERT: D 63 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7974 (m-40) REVERT: D 68 ASP cc_start: 0.8194 (t0) cc_final: 0.7923 (t70) REVERT: G 99 LYS cc_start: 0.8487 (mmtm) cc_final: 0.8239 (mmmt) REVERT: K 173 LYS cc_start: 0.5161 (mtmm) cc_final: 0.4863 (mtmt) REVERT: K 180 ARG cc_start: 0.4248 (tpm170) cc_final: 0.3776 (mtm180) REVERT: K 353 LYS cc_start: 0.3444 (mmpt) cc_final: 0.2916 (pttm) REVERT: K 430 MET cc_start: 0.6316 (mmp) cc_final: 0.5945 (mmm) REVERT: K 487 GLU cc_start: 0.4436 (mt-10) cc_final: 0.4088 (mt-10) REVERT: K 496 GLU cc_start: 0.5591 (mm-30) cc_final: 0.4679 (tp30) outliers start: 15 outliers final: 6 residues processed: 161 average time/residue: 0.3541 time to fit residues: 77.2659 Evaluate side-chains 133 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 126 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE 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: 0.8980 chunk 102 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN E 76 GLN F 25 ASN G 38 ASN K 499 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15861 Z= 0.223 Angle : 0.556 5.537 22634 Z= 0.329 Chirality : 0.035 0.137 2547 Planarity : 0.004 0.046 1861 Dihedral : 28.766 174.406 4411 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.44 % Allowed : 10.22 % Favored : 88.34 % 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 (0.26), residues: 1107 helix: 2.55 (0.20), residues: 663 sheet: 0.44 (0.68), residues: 58 loop : -1.23 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 363 HIS 0.005 0.001 HIS E 39 PHE 0.019 0.002 PHE G 25 TYR 0.013 0.002 TYR H 83 ARG 0.007 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.253 Fit side-chains REVERT: D 63 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8370 (t0) REVERT: D 68 ASP cc_start: 0.8373 (t0) cc_final: 0.8154 (t70) REVERT: G 99 LYS cc_start: 0.8538 (mmtm) cc_final: 0.8293 (mmmt) REVERT: K 173 LYS cc_start: 0.5245 (mtmm) cc_final: 0.4955 (mtmt) REVERT: K 373 TYR cc_start: 0.6445 (t80) cc_final: 0.6207 (t80) REVERT: K 430 MET cc_start: 0.6264 (mmp) cc_final: 0.6053 (mmm) REVERT: K 496 GLU cc_start: 0.5880 (mm-30) cc_final: 0.5611 (tp30) outliers start: 14 outliers final: 10 residues processed: 141 average time/residue: 0.3572 time to fit residues: 68.5015 Evaluate side-chains 139 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Chi-restraints excluded: chain K residue 499 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN F 25 ASN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15861 Z= 0.273 Angle : 0.580 5.145 22634 Z= 0.341 Chirality : 0.037 0.143 2547 Planarity : 0.004 0.041 1861 Dihedral : 28.826 175.220 4411 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.06 % Allowed : 11.46 % Favored : 86.48 % 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: 1.63 (0.25), residues: 1107 helix: 2.42 (0.20), residues: 662 sheet: 0.28 (0.68), residues: 60 loop : -1.27 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 363 HIS 0.006 0.001 HIS E 39 PHE 0.021 0.002 PHE C 25 TYR 0.014 0.002 TYR H 83 ARG 0.007 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.325 Fit side-chains REVERT: D 68 ASP cc_start: 0.8430 (t0) cc_final: 0.8200 (t70) REVERT: G 99 LYS cc_start: 0.8588 (mmtm) cc_final: 0.8313 (mmmt) REVERT: K 154 LEU cc_start: 0.3131 (OUTLIER) cc_final: 0.2774 (tt) REVERT: K 180 ARG cc_start: 0.4491 (tpm170) cc_final: 0.3856 (mtm180) REVERT: K 496 GLU cc_start: 0.6109 (mm-30) cc_final: 0.5677 (tp30) outliers start: 20 outliers final: 11 residues processed: 142 average time/residue: 0.3588 time to fit residues: 69.2554 Evaluate side-chains 132 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 446 SER Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 HIS H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15861 Z= 0.280 Angle : 0.578 5.220 22634 Z= 0.340 Chirality : 0.037 0.143 2547 Planarity : 0.004 0.041 1861 Dihedral : 28.868 175.229 4411 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.17 % Allowed : 12.49 % Favored : 85.35 % 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: 1.60 (0.25), residues: 1107 helix: 2.37 (0.20), residues: 665 sheet: 0.90 (0.68), residues: 55 loop : -1.36 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 363 HIS 0.006 0.001 HIS E 39 PHE 0.017 0.002 PHE C 25 TYR 0.011 0.002 TYR H 83 ARG 0.007 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 1.162 Fit side-chains REVERT: D 68 ASP cc_start: 0.8445 (t0) cc_final: 0.8220 (t70) REVERT: G 99 LYS cc_start: 0.8627 (mmtm) cc_final: 0.8338 (mmmt) REVERT: H 35 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: K 154 LEU cc_start: 0.2969 (OUTLIER) cc_final: 0.2616 (tt) REVERT: K 496 GLU cc_start: 0.6130 (mm-30) cc_final: 0.5914 (tp30) outliers start: 21 outliers final: 13 residues processed: 138 average time/residue: 0.3448 time to fit residues: 65.2939 Evaluate side-chains 131 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 446 SER Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 452 LEU Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE 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: 0.5980 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15861 Z= 0.174 Angle : 0.545 10.346 22634 Z= 0.324 Chirality : 0.035 0.172 2547 Planarity : 0.004 0.068 1861 Dihedral : 28.805 175.259 4411 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.24 % Allowed : 13.62 % Favored : 85.14 % 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: 2.58 (0.20), residues: 660 sheet: 0.95 (0.69), residues: 55 loop : -1.30 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 363 HIS 0.004 0.001 HIS E 39 PHE 0.013 0.002 PHE K 455 TYR 0.009 0.001 TYR F 51 ARG 0.010 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.166 Fit side-chains REVERT: D 68 ASP cc_start: 0.8393 (t0) cc_final: 0.8163 (t70) REVERT: G 99 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8332 (mmmt) REVERT: K 154 LEU cc_start: 0.2668 (OUTLIER) cc_final: 0.2423 (tt) REVERT: K 180 ARG cc_start: 0.4674 (tpm170) cc_final: 0.3907 (mtm180) REVERT: K 496 GLU cc_start: 0.6133 (mm-30) cc_final: 0.5668 (tp30) outliers start: 12 outliers final: 7 residues processed: 129 average time/residue: 0.3663 time to fit residues: 63.8859 Evaluate side-chains 123 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.0970 chunk 74 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 0.1980 chunk 80 optimal weight: 4.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- 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: 0.8129 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 15861 Z= 0.392 Angle : 0.651 7.860 22634 Z= 0.376 Chirality : 0.041 0.160 2547 Planarity : 0.005 0.058 1861 Dihedral : 29.102 174.780 4411 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.96 % Allowed : 13.62 % Favored : 84.42 % 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: 1.27 (0.25), residues: 1107 helix: 2.09 (0.20), residues: 666 sheet: 0.78 (0.69), residues: 55 loop : -1.48 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 431 HIS 0.007 0.001 HIS E 39 PHE 0.024 0.002 PHE K 455 TYR 0.012 0.002 TYR F 51 ARG 0.010 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 1.341 Fit side-chains REVERT: D 31 ARG cc_start: 0.4455 (ttt180) cc_final: 0.3795 (ttp-110) REVERT: D 68 ASP cc_start: 0.8525 (t0) cc_final: 0.8159 (t0) REVERT: F 91 LYS cc_start: 0.8458 (tttt) cc_final: 0.8121 (ttmm) REVERT: G 99 LYS cc_start: 0.8639 (mmtm) cc_final: 0.8285 (mmmt) REVERT: H 35 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7813 (mt-10) REVERT: K 154 LEU cc_start: 0.2843 (OUTLIER) cc_final: 0.2569 (tt) REVERT: K 180 ARG cc_start: 0.4691 (tpm170) cc_final: 0.3866 (mtm180) outliers start: 19 outliers final: 11 residues processed: 133 average time/residue: 0.3604 time to fit residues: 65.0629 Evaluate side-chains 126 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 420 SER Chi-restraints excluded: chain K residue 446 SER Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.8089 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15861 Z= 0.197 Angle : 0.578 7.393 22634 Z= 0.343 Chirality : 0.037 0.152 2547 Planarity : 0.004 0.073 1861 Dihedral : 28.997 174.872 4411 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.44 % Allowed : 14.55 % Favored : 84.00 % 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: 1.49 (0.25), residues: 1107 helix: 2.35 (0.20), residues: 658 sheet: 0.84 (0.69), residues: 55 loop : -1.47 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 318 HIS 0.005 0.001 HIS E 39 PHE 0.010 0.002 PHE C 25 TYR 0.012 0.001 TYR F 51 ARG 0.012 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.269 Fit side-chains REVERT: D 31 ARG cc_start: 0.4498 (ttt180) cc_final: 0.3850 (ttp-110) REVERT: D 68 ASP cc_start: 0.8467 (t0) cc_final: 0.8257 (t0) REVERT: F 91 LYS cc_start: 0.8390 (tttt) cc_final: 0.8052 (ttmm) REVERT: G 99 LYS cc_start: 0.8618 (mmtm) cc_final: 0.8307 (mmmt) REVERT: H 35 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: K 154 LEU cc_start: 0.2852 (OUTLIER) cc_final: 0.2570 (tt) REVERT: K 180 ARG cc_start: 0.4709 (tpm170) cc_final: 0.3946 (mtm180) REVERT: K 496 GLU cc_start: 0.6168 (mm-30) cc_final: 0.5897 (tp30) outliers start: 14 outliers final: 9 residues processed: 125 average time/residue: 0.3722 time to fit residues: 63.0473 Evaluate side-chains 121 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 110 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 420 SER Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 120 optimal weight: 0.0770 chunk 79 optimal weight: 5.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- 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: 0.8069 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15861 Z= 0.220 Angle : 0.550 7.410 22634 Z= 0.325 Chirality : 0.035 0.161 2547 Planarity : 0.004 0.061 1861 Dihedral : 28.791 174.757 4411 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.55 % Allowed : 14.24 % Favored : 84.21 % 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: 1.68 (0.25), residues: 1107 helix: 2.50 (0.20), residues: 659 sheet: 0.90 (0.70), residues: 55 loop : -1.40 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 318 HIS 0.005 0.001 HIS E 39 PHE 0.018 0.002 PHE K 449 TYR 0.008 0.001 TYR F 51 ARG 0.015 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.446 Fit side-chains REVERT: D 31 ARG cc_start: 0.4423 (ttt180) cc_final: 0.3805 (ttp-110) REVERT: D 68 ASP cc_start: 0.8414 (t0) cc_final: 0.8142 (t70) REVERT: F 91 LYS cc_start: 0.8420 (tttt) cc_final: 0.8062 (ttmm) REVERT: G 42 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7457 (ptm-80) REVERT: G 99 LYS cc_start: 0.8625 (mmtm) cc_final: 0.8327 (mmmt) REVERT: H 35 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: K 154 LEU cc_start: 0.2851 (OUTLIER) cc_final: 0.2560 (tt) REVERT: K 180 ARG cc_start: 0.4614 (tpm170) cc_final: 0.3891 (mtm180) REVERT: K 440 TRP cc_start: 0.4621 (m100) cc_final: 0.4374 (m100) REVERT: K 496 GLU cc_start: 0.6234 (mm-30) cc_final: 0.6001 (tp30) outliers start: 15 outliers final: 10 residues processed: 132 average time/residue: 0.4140 time to fit residues: 73.4748 Evaluate side-chains 126 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 420 SER Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 chunk 85 optimal weight: 7.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15861 Z= 0.254 Angle : 0.567 7.538 22634 Z= 0.334 Chirality : 0.036 0.162 2547 Planarity : 0.004 0.048 1861 Dihedral : 28.835 174.451 4411 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.55 % Allowed : 14.45 % Favored : 84.00 % 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: 1.60 (0.25), residues: 1107 helix: 2.44 (0.20), residues: 660 sheet: 0.90 (0.71), residues: 55 loop : -1.46 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 440 HIS 0.005 0.001 HIS E 39 PHE 0.013 0.002 PHE C 25 TYR 0.010 0.001 TYR F 51 ARG 0.012 0.000 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.378 Fit side-chains REVERT: D 31 ARG cc_start: 0.4534 (ttt180) cc_final: 0.3817 (ttp-110) REVERT: D 68 ASP cc_start: 0.8446 (t0) cc_final: 0.8181 (t70) REVERT: F 91 LYS cc_start: 0.8417 (tttt) cc_final: 0.8065 (ttmm) REVERT: G 42 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7482 (ptm-80) REVERT: G 99 LYS cc_start: 0.8633 (mmtm) cc_final: 0.8335 (mmmt) REVERT: H 35 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7767 (mt-10) REVERT: K 154 LEU cc_start: 0.2888 (OUTLIER) cc_final: 0.2588 (tt) REVERT: K 440 TRP cc_start: 0.4806 (m100) cc_final: 0.4460 (m100) REVERT: K 441 ASP cc_start: 0.1292 (OUTLIER) cc_final: 0.0759 (m-30) outliers start: 15 outliers final: 10 residues processed: 130 average time/residue: 0.3735 time to fit residues: 65.5234 Evaluate side-chains 128 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 420 SER Chi-restraints excluded: chain K residue 423 VAL Chi-restraints excluded: chain K residue 441 ASP Chi-restraints excluded: chain K residue 457 LEU Chi-restraints excluded: chain K residue 481 ILE 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: 3.9990 chunk 98 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.0870 chunk 107 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.150246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112084 restraints weight = 22010.398| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.40 r_work: 0.2881 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15861 Z= 0.166 Angle : 0.541 7.518 22634 Z= 0.323 Chirality : 0.035 0.155 2547 Planarity : 0.004 0.039 1861 Dihedral : 28.805 174.324 4411 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.24 % Allowed : 14.65 % Favored : 84.11 % 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: 2.59 (0.20), residues: 660 sheet: 0.97 (0.71), residues: 55 loop : -1.37 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 440 HIS 0.004 0.001 HIS E 39 PHE 0.022 0.001 PHE K 449 TYR 0.017 0.001 TYR K 495 ARG 0.007 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2735.19 seconds wall clock time: 49 minutes 30.34 seconds (2970.34 seconds total)