Starting phenix.real_space_refine on Mon Apr 8 02:08:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/04_2024/6rjg_4904.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/04_2024/6rjg_4904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/04_2024/6rjg_4904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/04_2024/6rjg_4904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/04_2024/6rjg_4904.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rjg_4904/04_2024/6rjg_4904.pdb" } resolution = 3.2 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 123 5.49 5 S 37 5.16 5 C 7318 2.51 5 N 2103 2.21 5 O 2639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 5": "OD1" <-> "OD2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 156": "OD1" <-> "OD2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 156": "OD1" <-> "OD2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "C ASP 3": "OD1" <-> "OD2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C ARG 46": "NH1" <-> "NH2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C GLU 157": "OE1" <-> "OE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C ARG 235": "NH1" <-> "NH2" Residue "C ARG 240": "NH1" <-> "NH2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C ARG 267": "NH1" <-> "NH2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C GLU 351": "OE1" <-> "OE2" Residue "C ARG 354": "NH1" <-> "NH2" Residue "C ASP 363": "OD1" <-> "OD2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C GLU 390": "OE1" <-> "OE2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "C GLU 408": "OE1" <-> "OE2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C ASP 469": "OD1" <-> "OD2" Residue "C GLU 470": "OE1" <-> "OE2" Residue "C GLU 475": "OE1" <-> "OE2" Residue "C GLU 476": "OE1" <-> "OE2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C GLU 499": "OE1" <-> "OE2" Residue "C ASP 502": "OD1" <-> "OD2" Residue "C ARG 703": "NH1" <-> "NH2" Residue "C ASP 815": "OD1" <-> "OD2" Residue "C PHE 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 824": "OD1" <-> "OD2" Residue "C ARG 831": "NH1" <-> "NH2" Residue "C ASP 838": "OD1" <-> "OD2" Residue "C ARG 876": "NH1" <-> "NH2" Residue "C GLU 916": "OE1" <-> "OE2" Residue "C ARG 921": "NH1" <-> "NH2" Residue "C ARG 966": "NH1" <-> "NH2" Residue "C GLU 1011": "OE1" <-> "OE2" Residue "C GLU 1018": "OE1" <-> "OE2" Residue "C GLU 1035": "OE1" <-> "OE2" Residue "C GLU 1067": "OE1" <-> "OE2" Residue "C GLU 1070": "OE1" <-> "OE2" Residue "C TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12220 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "B" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1506 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "C" Number of atoms: 6633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6633 Classifications: {'peptide': 814} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 794} Chain breaks: 5 Chain: "D" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1656 Classifications: {'RNA': 78} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 32} Link IDs: {'rna2p': 9, 'rna3p': 68} Chain breaks: 2 Chain: "E" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 646 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "G" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 273 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Time building chain proxies: 6.85, per 1000 atoms: 0.56 Number of scatterers: 12220 At special positions: 0 Unit cell: (121.793, 140.462, 111.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 123 15.00 O 2639 8.00 N 2103 7.00 C 7318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.31 Conformation dependent library (CDL) restraints added in 1.7 seconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2206 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 47.7% alpha, 14.4% beta 38 base pairs and 80 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 removed outlier: 3.621A pdb=" N LYS A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.836A pdb=" N ASP A 24 " --> pdb=" O PHE A 21 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A 26 " --> pdb=" O ASN A 23 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 27 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 28 " --> pdb=" O PHE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.675A pdb=" N LEU A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 81 removed outlier: 3.896A pdb=" N ASN A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 4.163A pdb=" N LYS A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.935A pdb=" N GLY A 146 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 147 " --> pdb=" O GLY A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 147' Processing helix chain 'A' and resid 167 through 178 removed outlier: 3.559A pdb=" N GLU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 19 removed outlier: 3.617A pdb=" N LYS B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 removed outlier: 3.833A pdb=" N TYR B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 43 removed outlier: 3.554A pdb=" N ASN B 43 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.688A pdb=" N LEU B 63 " --> pdb=" O MET B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 80 Processing helix chain 'B' and resid 82 through 89 removed outlier: 4.128A pdb=" N LYS B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 110 removed outlier: 3.716A pdb=" N TYR B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 110 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.759A pdb=" N ARG B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 73 removed outlier: 3.757A pdb=" N VAL C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 98 Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 134 through 145 removed outlier: 3.674A pdb=" N GLN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 185 through 204 removed outlier: 3.748A pdb=" N TYR C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.346A pdb=" N ILE C 254 " --> pdb=" O ASN C 250 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU C 255 " --> pdb=" O ILE C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 255' Processing helix chain 'C' and resid 272 through 285 removed outlier: 3.922A pdb=" N GLN C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 311 Processing helix chain 'C' and resid 315 through 328 removed outlier: 3.949A pdb=" N LEU C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 358 removed outlier: 3.755A pdb=" N THR C 358 " --> pdb=" O ARG C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 382 removed outlier: 3.521A pdb=" N ASN C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 396 removed outlier: 3.737A pdb=" N PHE C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 416 removed outlier: 3.644A pdb=" N ASN C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.832A pdb=" N PHE C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 436 Processing helix chain 'C' and resid 445 through 453 Processing helix chain 'C' and resid 469 through 474 removed outlier: 3.801A pdb=" N LEU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 500 removed outlier: 3.568A pdb=" N ALA C 483 " --> pdb=" O ASN C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 705 Processing helix chain 'C' and resid 854 through 868 Processing helix chain 'C' and resid 869 through 872 removed outlier: 3.687A pdb=" N PHE C 872 " --> pdb=" O LYS C 869 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 869 through 872' Processing helix chain 'C' and resid 873 through 878 Processing helix chain 'C' and resid 878 through 892 removed outlier: 3.594A pdb=" N PHE C 882 " --> pdb=" O ASP C 878 " (cutoff:3.500A) Proline residue: C 888 - end of helix Processing helix chain 'C' and resid 910 through 918 Processing helix chain 'C' and resid 986 through 988 No H-bonds generated for 'chain 'C' and resid 986 through 988' Processing helix chain 'C' and resid 1000 through 1011 Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 122 removed outlier: 6.776A pdb=" N ILE A 115 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 136 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY A 117 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU A 134 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 119 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET A 121 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA A 130 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 122 removed outlier: 6.776A pdb=" N ILE A 115 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 136 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLY A 117 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU A 134 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 119 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET A 121 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA A 130 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N TYR A 128 " --> pdb=" O ASP C 947 " (cutoff:3.500A) removed outlier: 11.901A pdb=" N ILE C 827 " --> pdb=" O LYS C 848 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N LYS C 848 " --> pdb=" O ILE C 827 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA C 829 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THR C 843 " --> pdb=" O LYS C 941 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LYS C 941 " --> pdb=" O THR C 843 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C 845 " --> pdb=" O ASP C 939 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 114 through 122 removed outlier: 7.535A pdb=" N MET B 121 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN B 131 " --> pdb=" O MET B 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 710 through 713 removed outlier: 3.919A pdb=" N HIS C 29 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N LEU C 809 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS C 30 " --> pdb=" O LEU C 809 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N SER C 811 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER C 32 " --> pdb=" O SER C 811 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 268 through 269 removed outlier: 3.586A pdb=" N ALA C 268 " --> pdb=" O HIS C 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 338 through 339 removed outlier: 3.805A pdb=" N ARG C 338 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 978 through 980 removed outlier: 7.039A pdb=" N LEU C 983 " --> pdb=" O TRP C 965 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 978 through 980 removed outlier: 3.561A pdb=" N PHE C1021 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE C 971 " --> pdb=" O PHE C1019 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE C1019 " --> pdb=" O PHE C 971 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 989 through 990 Processing sheet with id=AB1, first strand: chain 'C' and resid 1085 through 1088 removed outlier: 4.515A pdb=" N CYS C1085 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLU C1057 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C1028 " --> pdb=" O VAL C1099 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 90 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 80 stacking parallelities Total time for adding SS restraints: 4.83 Time building geometry restraints manager: 5.73 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: 2561 1.33 - 1.45: 3525 1.45 - 1.57: 6301 1.57 - 1.70: 241 1.70 - 1.82: 69 Bond restraints: 12697 Sorted by residual: bond pdb=" CA ASN B 83 " pdb=" C ASN B 83 " ideal model delta sigma weight residual 1.522 1.558 -0.036 1.72e-02 3.38e+03 4.44e+00 bond pdb=" CB ARG C 267 " pdb=" CG ARG C 267 " ideal model delta sigma weight residual 1.520 1.457 0.063 3.00e-02 1.11e+03 4.37e+00 bond pdb=" CG LEU C 959 " pdb=" CD1 LEU C 959 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.34e+00 bond pdb=" CB LYS C1010 " pdb=" CG LYS C1010 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.29e+00 bond pdb=" CA GLU C 887 " pdb=" C GLU C 887 " ideal model delta sigma weight residual 1.520 1.540 -0.020 1.23e-02 6.61e+03 2.59e+00 ... (remaining 12692 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.52: 698 105.52 - 112.95: 6698 112.95 - 120.37: 5478 120.37 - 127.79: 4524 127.79 - 135.22: 228 Bond angle restraints: 17626 Sorted by residual: angle pdb=" CA TYR A 26 " pdb=" CB TYR A 26 " pdb=" CG TYR A 26 " ideal model delta sigma weight residual 113.90 122.15 -8.25 1.80e+00 3.09e-01 2.10e+01 angle pdb=" CA ILE C 436 " pdb=" C ILE C 436 " pdb=" N PRO C 437 " ideal model delta sigma weight residual 118.88 124.84 -5.96 1.54e+00 4.22e-01 1.50e+01 angle pdb=" C HIS C 705 " pdb=" N LYS C 706 " pdb=" CA LYS C 706 " ideal model delta sigma weight residual 122.36 127.36 -5.00 1.42e+00 4.96e-01 1.24e+01 angle pdb=" CA LYS C 706 " pdb=" CB LYS C 706 " pdb=" CG LYS C 706 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA GLU C1113 " pdb=" CB GLU C1113 " pdb=" CG GLU C1113 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 ... (remaining 17621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 6371 17.72 - 35.44: 859 35.44 - 53.16: 300 53.16 - 70.88: 115 70.88 - 88.60: 29 Dihedral angle restraints: 7674 sinusoidal: 4227 harmonic: 3447 Sorted by residual: dihedral pdb=" CA ILE C 334 " pdb=" C ILE C 334 " pdb=" N LYS C 335 " pdb=" CA LYS C 335 " ideal model delta harmonic sigma weight residual 180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA HIS C 348 " pdb=" C HIS C 348 " pdb=" N THR C 349 " pdb=" CA THR C 349 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA MET A 87 " pdb=" C MET A 87 " pdb=" N ASN A 88 " pdb=" CA ASN A 88 " ideal model delta harmonic sigma weight residual -180.00 -157.66 -22.34 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 7671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1707 0.082 - 0.165: 236 0.165 - 0.247: 21 0.247 - 0.330: 3 0.330 - 0.412: 2 Chirality restraints: 1969 Sorted by residual: chirality pdb=" CB ILE B 48 " pdb=" CA ILE B 48 " pdb=" CG1 ILE B 48 " pdb=" CG2 ILE B 48 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB ILE A 48 " pdb=" CA ILE A 48 " pdb=" CG1 ILE A 48 " pdb=" CG2 ILE A 48 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CB ILE C 999 " pdb=" CA ILE C 999 " pdb=" CG1 ILE C 999 " pdb=" CG2 ILE C 999 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1966 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 260 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.44e+00 pdb=" C THR C 260 " 0.053 2.00e-02 2.50e+03 pdb=" O THR C 260 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE C 261 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U D 7 " 0.034 2.00e-02 2.50e+03 2.05e-02 9.42e+00 pdb=" N1 U D 7 " -0.049 2.00e-02 2.50e+03 pdb=" C2 U D 7 " 0.007 2.00e-02 2.50e+03 pdb=" O2 U D 7 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U D 7 " 0.000 2.00e-02 2.50e+03 pdb=" C4 U D 7 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U D 7 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U D 7 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U D 7 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 26 " -0.025 2.00e-02 2.50e+03 1.83e-02 6.72e+00 pdb=" CG TYR B 26 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B 26 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 26 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 26 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 26 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 26 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 26 " -0.001 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3439 2.82 - 3.34: 9580 3.34 - 3.86: 19773 3.86 - 4.38: 23494 4.38 - 4.90: 38482 Nonbonded interactions: 94768 Sorted by model distance: nonbonded pdb=" OD2 ASP C 878 " pdb=" OG1 THR C 881 " model vdw 2.297 2.440 nonbonded pdb=" OE2 GLU A 68 " pdb=" NZ LYS A 99 " model vdw 2.339 2.520 nonbonded pdb=" OE1 GLU B 135 " pdb=" NE2 GLN B 151 " model vdw 2.341 2.520 nonbonded pdb=" OG1 THR C 830 " pdb=" O LYS C 956 " model vdw 2.362 2.440 nonbonded pdb=" O ALA C 376 " pdb=" OG1 THR C 380 " model vdw 2.377 2.440 ... (remaining 94763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.260 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 37.410 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 0.071 12697 Z= 0.511 Angle : 0.955 12.264 17626 Z= 0.526 Chirality : 0.059 0.412 1969 Planarity : 0.006 0.063 1818 Dihedral : 18.835 88.602 5468 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.10 % Allowed : 6.79 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.18), residues: 1164 helix: -2.16 (0.17), residues: 504 sheet: -1.79 (0.34), residues: 143 loop : -2.74 (0.21), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 38 HIS 0.010 0.002 HIS C 425 PHE 0.023 0.003 PHE C 818 TYR 0.043 0.003 TYR B 26 ARG 0.013 0.001 ARG C 921 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: B 15 MET cc_start: 0.7669 (tmm) cc_final: 0.7324 (tmm) REVERT: B 155 LYS cc_start: 0.7389 (tptt) cc_final: 0.7167 (tptt) REVERT: B 156 ASP cc_start: 0.7732 (p0) cc_final: 0.7448 (t0) REVERT: C 273 TYR cc_start: 0.8173 (t80) cc_final: 0.7966 (t80) REVERT: C 447 MET cc_start: 0.6645 (ttt) cc_final: 0.6324 (ttp) REVERT: C 869 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8398 (tttt) REVERT: C 877 HIS cc_start: 0.6938 (m170) cc_final: 0.6612 (t-90) outliers start: 1 outliers final: 1 residues processed: 200 average time/residue: 0.3017 time to fit residues: 81.9673 Evaluate side-chains 150 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.0270 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 177 ASN B 88 ASN B 151 GLN B 177 ASN B 178 ASN C 85 ASN C 142 ASN C 227 HIS C 276 GLN C 456 GLN C 505 ASN C 832 GLN C 855 GLN C 944 ASN C 945 HIS C1001 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12697 Z= 0.147 Angle : 0.536 7.553 17626 Z= 0.297 Chirality : 0.037 0.163 1969 Planarity : 0.004 0.035 1818 Dihedral : 18.719 79.359 2992 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.34 % Allowed : 12.33 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.21), residues: 1164 helix: 0.04 (0.21), residues: 509 sheet: -1.36 (0.36), residues: 140 loop : -2.45 (0.22), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.005 0.001 HIS C 178 PHE 0.011 0.001 PHE A 67 TYR 0.023 0.001 TYR B 26 ARG 0.005 0.000 ARG C 369 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 168 time to evaluate : 1.192 Fit side-chains REVERT: B 15 MET cc_start: 0.7760 (tmm) cc_final: 0.7528 (tmm) REVERT: B 156 ASP cc_start: 0.7515 (p0) cc_final: 0.7244 (t70) REVERT: C 447 MET cc_start: 0.6532 (ttt) cc_final: 0.6161 (ttp) REVERT: C 877 HIS cc_start: 0.6870 (m170) cc_final: 0.6416 (t-90) REVERT: C 1011 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7320 (mm-30) outliers start: 14 outliers final: 8 residues processed: 178 average time/residue: 0.2824 time to fit residues: 69.8861 Evaluate side-chains 154 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 ASN C 877 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 12697 Z= 0.467 Angle : 0.703 11.789 17626 Z= 0.375 Chirality : 0.045 0.186 1969 Planarity : 0.005 0.045 1818 Dihedral : 18.747 80.274 2989 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.21 % Allowed : 13.67 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.22), residues: 1164 helix: 0.48 (0.22), residues: 512 sheet: -1.24 (0.38), residues: 141 loop : -2.44 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 174 HIS 0.004 0.001 HIS C 425 PHE 0.019 0.002 PHE C1044 TYR 0.026 0.002 TYR B 80 ARG 0.007 0.001 ARG C 369 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 147 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: B 15 MET cc_start: 0.7864 (tmm) cc_final: 0.7616 (tmm) REVERT: B 139 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7710 (mm-30) REVERT: B 155 LYS cc_start: 0.7492 (tptt) cc_final: 0.7248 (tptt) REVERT: C 877 HIS cc_start: 0.7097 (m-70) cc_final: 0.6512 (t-90) REVERT: C 1011 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7447 (mm-30) REVERT: C 1055 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.8341 (m-10) outliers start: 44 outliers final: 28 residues processed: 177 average time/residue: 0.2616 time to fit residues: 65.5451 Evaluate side-chains 170 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 508 ILE Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 0.0030 chunk 33 optimal weight: 4.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN C1001 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12697 Z= 0.197 Angle : 0.541 8.947 17626 Z= 0.295 Chirality : 0.038 0.151 1969 Planarity : 0.003 0.034 1818 Dihedral : 18.579 79.811 2989 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.06 % Allowed : 15.58 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1164 helix: 1.04 (0.22), residues: 513 sheet: -0.98 (0.39), residues: 144 loop : -2.26 (0.23), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 174 HIS 0.002 0.001 HIS C 178 PHE 0.011 0.001 PHE C 882 TYR 0.019 0.001 TYR B 26 ARG 0.006 0.000 ARG C 369 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 101 GLN cc_start: 0.7801 (pt0) cc_final: 0.7496 (mt0) REVERT: A 149 MET cc_start: 0.9086 (tpt) cc_final: 0.8769 (tpt) REVERT: B 15 MET cc_start: 0.7787 (tmm) cc_final: 0.7543 (tmm) REVERT: B 155 LYS cc_start: 0.7298 (tptt) cc_final: 0.7023 (tptt) REVERT: C 447 MET cc_start: 0.6416 (ttt) cc_final: 0.6094 (ttp) REVERT: C 877 HIS cc_start: 0.7105 (m-70) cc_final: 0.6376 (t-90) REVERT: C 991 GLU cc_start: 0.7653 (tt0) cc_final: 0.7300 (tt0) REVERT: C 999 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8648 (tp) REVERT: C 1011 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7384 (mm-30) REVERT: C 1055 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8521 (m-10) outliers start: 32 outliers final: 20 residues processed: 174 average time/residue: 0.2662 time to fit residues: 65.6410 Evaluate side-chains 165 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 999 ILE Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN B 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12697 Z= 0.241 Angle : 0.562 11.226 17626 Z= 0.305 Chirality : 0.039 0.152 1969 Planarity : 0.003 0.035 1818 Dihedral : 18.529 79.662 2989 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.54 % Allowed : 15.58 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.23), residues: 1164 helix: 1.23 (0.22), residues: 515 sheet: -0.87 (0.41), residues: 141 loop : -2.19 (0.23), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 174 HIS 0.002 0.001 HIS C 425 PHE 0.010 0.001 PHE C 882 TYR 0.019 0.002 TYR B 26 ARG 0.006 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 151 time to evaluate : 1.299 Fit side-chains REVERT: A 101 GLN cc_start: 0.7856 (pt0) cc_final: 0.7544 (mt0) REVERT: A 149 MET cc_start: 0.9090 (tpt) cc_final: 0.8770 (tpt) REVERT: B 15 MET cc_start: 0.7800 (tmm) cc_final: 0.7541 (tmm) REVERT: B 111 ARG cc_start: 0.7593 (tpt-90) cc_final: 0.7303 (tpt-90) REVERT: C 39 GLN cc_start: 0.8486 (pm20) cc_final: 0.8082 (pm20) REVERT: C 447 MET cc_start: 0.6449 (ttt) cc_final: 0.6129 (ttp) REVERT: C 869 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8343 (ttmt) REVERT: C 877 HIS cc_start: 0.7110 (m-70) cc_final: 0.6368 (t-90) REVERT: C 991 GLU cc_start: 0.7635 (tt0) cc_final: 0.7368 (tt0) REVERT: C 999 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8641 (tp) REVERT: C 1011 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7385 (mm-30) REVERT: C 1055 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.8576 (m-10) outliers start: 37 outliers final: 26 residues processed: 180 average time/residue: 0.2826 time to fit residues: 72.2426 Evaluate side-chains 174 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 999 ILE Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 0.0270 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN B 151 GLN C 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12697 Z= 0.128 Angle : 0.486 7.702 17626 Z= 0.267 Chirality : 0.036 0.175 1969 Planarity : 0.003 0.033 1818 Dihedral : 18.385 79.247 2989 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.58 % Allowed : 18.45 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1164 helix: 1.58 (0.23), residues: 515 sheet: -0.61 (0.41), residues: 145 loop : -1.96 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 174 HIS 0.002 0.000 HIS C 425 PHE 0.013 0.001 PHE C 261 TYR 0.014 0.001 TYR B 26 ARG 0.009 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 101 GLN cc_start: 0.7773 (pt0) cc_final: 0.7525 (mt0) REVERT: A 149 MET cc_start: 0.9083 (tpt) cc_final: 0.8760 (tpt) REVERT: B 15 MET cc_start: 0.7713 (tmm) cc_final: 0.7423 (tmm) REVERT: B 111 ARG cc_start: 0.7507 (tpt-90) cc_final: 0.7273 (tpt-90) REVERT: C 39 GLN cc_start: 0.8463 (pm20) cc_final: 0.8193 (pm20) REVERT: C 157 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7071 (mt-10) REVERT: C 447 MET cc_start: 0.6236 (ttt) cc_final: 0.5944 (ttp) REVERT: C 862 MET cc_start: 0.8061 (tpp) cc_final: 0.7547 (mpp) REVERT: C 877 HIS cc_start: 0.6996 (m-70) cc_final: 0.6347 (t-90) REVERT: C 991 GLU cc_start: 0.7621 (tt0) cc_final: 0.7304 (tt0) REVERT: C 1011 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7353 (mm-30) outliers start: 27 outliers final: 18 residues processed: 182 average time/residue: 0.2648 time to fit residues: 67.2732 Evaluate side-chains 172 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 GLN C 403 GLN ** C 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12697 Z= 0.364 Angle : 0.635 14.442 17626 Z= 0.340 Chirality : 0.042 0.163 1969 Planarity : 0.004 0.037 1818 Dihedral : 18.515 80.424 2989 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.82 % Allowed : 17.59 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.24), residues: 1164 helix: 1.37 (0.23), residues: 512 sheet: -0.82 (0.41), residues: 142 loop : -2.08 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 174 HIS 0.002 0.001 HIS C 348 PHE 0.014 0.002 PHE C1044 TYR 0.021 0.002 TYR A 128 ARG 0.006 0.001 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 1.219 Fit side-chains revert: symmetry clash REVERT: A 101 GLN cc_start: 0.7884 (pt0) cc_final: 0.7553 (mt0) REVERT: B 111 ARG cc_start: 0.7611 (tpt-90) cc_final: 0.7330 (tpt-90) REVERT: B 134 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7581 (tt) REVERT: C 447 MET cc_start: 0.6515 (ttt) cc_final: 0.6187 (ttp) REVERT: C 869 LYS cc_start: 0.8753 (ttmt) cc_final: 0.8359 (ttmt) REVERT: C 981 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8784 (mp) REVERT: C 991 GLU cc_start: 0.7654 (tt0) cc_final: 0.7330 (tt0) REVERT: C 1011 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7417 (mm-30) outliers start: 40 outliers final: 30 residues processed: 167 average time/residue: 0.2617 time to fit residues: 62.6579 Evaluate side-chains 171 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 508 ILE Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 78 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12697 Z= 0.194 Angle : 0.532 11.849 17626 Z= 0.288 Chirality : 0.038 0.160 1969 Planarity : 0.003 0.035 1818 Dihedral : 18.406 80.182 2989 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.92 % Allowed : 17.78 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1164 helix: 1.47 (0.23), residues: 516 sheet: -0.67 (0.41), residues: 145 loop : -1.95 (0.24), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 174 HIS 0.002 0.001 HIS C 425 PHE 0.012 0.001 PHE C 261 TYR 0.017 0.001 TYR B 26 ARG 0.007 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 144 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 101 GLN cc_start: 0.7832 (pt0) cc_final: 0.7544 (mt0) REVERT: A 156 ASP cc_start: 0.8079 (p0) cc_final: 0.7827 (p0) REVERT: B 28 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8310 (mt) REVERT: B 111 ARG cc_start: 0.7487 (tpt-90) cc_final: 0.7225 (tpt-90) REVERT: C 447 MET cc_start: 0.6455 (ttt) cc_final: 0.6160 (ttp) REVERT: C 450 LEU cc_start: 0.7164 (mt) cc_final: 0.6836 (mt) REVERT: C 869 LYS cc_start: 0.8726 (ttmt) cc_final: 0.8340 (ttmt) REVERT: C 991 GLU cc_start: 0.7621 (tt0) cc_final: 0.7312 (tt0) REVERT: C 1011 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7334 (mm-30) outliers start: 41 outliers final: 31 residues processed: 174 average time/residue: 0.2597 time to fit residues: 64.8185 Evaluate side-chains 183 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12697 Z= 0.257 Angle : 0.569 14.359 17626 Z= 0.305 Chirality : 0.039 0.157 1969 Planarity : 0.003 0.035 1818 Dihedral : 18.458 80.199 2989 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.02 % Allowed : 17.69 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.24), residues: 1164 helix: 1.43 (0.23), residues: 517 sheet: -0.69 (0.42), residues: 142 loop : -2.02 (0.24), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 174 HIS 0.002 0.001 HIS C 348 PHE 0.011 0.002 PHE C 412 TYR 0.017 0.002 TYR B 26 ARG 0.006 0.000 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 1.230 Fit side-chains REVERT: A 101 GLN cc_start: 0.7838 (pt0) cc_final: 0.7544 (mt0) REVERT: A 149 MET cc_start: 0.9113 (tpt) cc_final: 0.8839 (tpp) REVERT: A 156 ASP cc_start: 0.8135 (p0) cc_final: 0.7862 (p0) REVERT: B 28 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8418 (mt) REVERT: B 111 ARG cc_start: 0.7411 (tpt-90) cc_final: 0.7135 (tpt-90) REVERT: C 39 GLN cc_start: 0.8515 (pm20) cc_final: 0.7684 (pm20) REVERT: C 375 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8167 (tp) REVERT: C 447 MET cc_start: 0.6496 (ttt) cc_final: 0.6181 (ttp) REVERT: C 877 HIS cc_start: 0.7072 (m-70) cc_final: 0.6384 (t-90) REVERT: C 991 GLU cc_start: 0.7629 (tt0) cc_final: 0.7313 (tt0) REVERT: C 1011 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7366 (mm-30) outliers start: 42 outliers final: 35 residues processed: 173 average time/residue: 0.2473 time to fit residues: 61.7471 Evaluate side-chains 184 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 147 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 924 SER Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12697 Z= 0.220 Angle : 0.548 13.642 17626 Z= 0.295 Chirality : 0.038 0.160 1969 Planarity : 0.003 0.035 1818 Dihedral : 18.441 80.169 2989 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.82 % Allowed : 17.88 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1164 helix: 1.48 (0.23), residues: 517 sheet: -0.66 (0.42), residues: 145 loop : -1.99 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 174 HIS 0.001 0.001 HIS C 705 PHE 0.012 0.001 PHE C 412 TYR 0.017 0.001 TYR B 26 ARG 0.007 0.000 ARG C 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 151 time to evaluate : 1.316 Fit side-chains REVERT: A 101 GLN cc_start: 0.7832 (pt0) cc_final: 0.7552 (mt0) REVERT: A 149 MET cc_start: 0.9108 (tpt) cc_final: 0.8840 (tpp) REVERT: A 156 ASP cc_start: 0.8081 (p0) cc_final: 0.7834 (p0) REVERT: B 28 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8336 (mt) REVERT: B 111 ARG cc_start: 0.7389 (tpt-90) cc_final: 0.7126 (tpt-90) REVERT: B 134 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7439 (tt) REVERT: C 39 GLN cc_start: 0.8478 (pm20) cc_final: 0.7666 (pm20) REVERT: C 375 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8192 (tp) REVERT: C 447 MET cc_start: 0.6472 (ttt) cc_final: 0.6166 (ttp) REVERT: C 862 MET cc_start: 0.8026 (tpp) cc_final: 0.7568 (mpp) REVERT: C 877 HIS cc_start: 0.7049 (m-70) cc_final: 0.6360 (t-90) REVERT: C 991 GLU cc_start: 0.7621 (tt0) cc_final: 0.7325 (tt0) REVERT: C 1011 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7349 (mm-30) outliers start: 40 outliers final: 36 residues processed: 180 average time/residue: 0.2465 time to fit residues: 63.9677 Evaluate side-chains 190 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 440 TYR Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 711 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1070 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 101 optimal weight: 0.0030 chunk 42 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN C 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.160352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126884 restraints weight = 16861.876| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.32 r_work: 0.3212 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12697 Z= 0.130 Angle : 0.486 10.799 17626 Z= 0.263 Chirality : 0.035 0.144 1969 Planarity : 0.003 0.033 1818 Dihedral : 18.333 78.938 2989 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.77 % Allowed : 19.50 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.25), residues: 1164 helix: 1.74 (0.23), residues: 517 sheet: -0.47 (0.43), residues: 145 loop : -1.86 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 174 HIS 0.002 0.000 HIS C 945 PHE 0.011 0.001 PHE C 412 TYR 0.016 0.001 TYR B 26 ARG 0.007 0.000 ARG C 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2649.35 seconds wall clock time: 49 minutes 13.33 seconds (2953.33 seconds total)