Starting phenix.real_space_refine on Fri Sep 27 10:00:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzy_26922/09_2024/7uzy_26922.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzy_26922/09_2024/7uzy_26922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzy_26922/09_2024/7uzy_26922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzy_26922/09_2024/7uzy_26922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzy_26922/09_2024/7uzy_26922.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzy_26922/09_2024/7uzy_26922.cif" } resolution = 4.05 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= 0.029 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 44 5.49 5 S 39 5.16 5 C 9578 2.51 5 N 2599 2.21 5 O 3072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15332 Number of models: 1 Model: "" Number of chains: 11 Chain: "F" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3353 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 3, 'TRANS': 410} Chain breaks: 7 Chain: "J" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 871 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 2 Chain: "I" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 937 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain breaks: 1 Chain: "K" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 505 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain breaks: 1 Chain: "D" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1572 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 4, 'TRANS': 193} Chain breaks: 1 Chain: "C" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "A" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "B" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1523 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 2 Chain: "H" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2378 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 1 Chain: "G" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 637 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 10, 'rna3p': 19} Chain: "L" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 10} Chain breaks: 1 Time building chain proxies: 10.44, per 1000 atoms: 0.68 Number of scatterers: 15332 At special positions: 0 Unit cell: (96.8, 122.1, 188.1, 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 39 16.00 P 44 15.00 O 3072 8.00 N 2599 7.00 C 9578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 407 " - pdb=" SG CYS F 423 " distance=1.90 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 426 " distance=2.03 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: 4.53 Conformation dependent library (CDL) restraints added in 1.9 seconds 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3326 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 21 sheets defined 47.7% alpha, 17.0% beta 10 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 13 through 15 No H-bonds generated for 'chain 'F' and resid 13 through 15' Processing helix chain 'F' and resid 16 through 22 removed outlier: 3.999A pdb=" N ILE F 20 " --> pdb=" O ILE F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 42 removed outlier: 3.539A pdb=" N LEU F 36 " --> pdb=" O THR F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 58 removed outlier: 3.770A pdb=" N LEU F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 66 removed outlier: 4.129A pdb=" N LYS F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 153 through 170 Processing helix chain 'F' and resid 177 through 190 removed outlier: 3.887A pdb=" N GLN F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 227 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 244 through 249 Processing helix chain 'F' and resid 261 through 267 Processing helix chain 'F' and resid 273 through 300 Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 322 through 344 Processing helix chain 'F' and resid 358 through 363 removed outlier: 3.959A pdb=" N LEU F 362 " --> pdb=" O SER F 358 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET F 363 " --> pdb=" O GLY F 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 358 through 363' Processing helix chain 'F' and resid 367 through 384 removed outlier: 3.689A pdb=" N THR F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 398 removed outlier: 3.538A pdb=" N HIS F 398 " --> pdb=" O LEU F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 424 through 437 removed outlier: 4.293A pdb=" N ARG F 437 " --> pdb=" O SER F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 470 Processing helix chain 'F' and resid 552 through 566 Processing helix chain 'J' and resid 18 through 24 Processing helix chain 'J' and resid 44 through 47 Processing helix chain 'J' and resid 48 through 61 Processing helix chain 'J' and resid 75 through 92 removed outlier: 3.575A pdb=" N GLU J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 102 Processing helix chain 'J' and resid 103 through 115 Processing helix chain 'J' and resid 116 through 137 Processing helix chain 'I' and resid 15 through 24 removed outlier: 3.794A pdb=" N VAL I 20 " --> pdb=" O PHE I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 47 Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 92 through 102 Processing helix chain 'I' and resid 103 through 115 Processing helix chain 'I' and resid 116 through 137 Processing helix chain 'K' and resid 44 through 47 Processing helix chain 'K' and resid 48 through 59 Processing helix chain 'K' and resid 73 through 92 Processing helix chain 'K' and resid 92 through 102 Processing helix chain 'K' and resid 103 through 112 Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 66 through 73 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 104 through 114 Processing helix chain 'D' and resid 161 through 178 Processing helix chain 'C' and resid 47 through 63 removed outlier: 4.108A pdb=" N ILE C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 removed outlier: 4.301A pdb=" N HIS C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 104 through 115 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 161 through 178 removed outlier: 4.098A pdb=" N ASP C 165 " --> pdb=" O GLN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'A' and resid 47 through 63 removed outlier: 3.775A pdb=" N PHE A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 removed outlier: 3.809A pdb=" N HIS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 161 through 178 removed outlier: 3.585A pdb=" N ASN A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'B' and resid 47 through 63 removed outlier: 3.768A pdb=" N PHE B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 161 through 178 Processing helix chain 'H' and resid 31 through 47 Processing helix chain 'H' and resid 50 through 55 Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 110 through 120 Processing helix chain 'H' and resid 168 through 183 Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 231 through 236 Processing sheet with id=AA1, first strand: chain 'F' and resid 307 through 311 removed outlier: 5.981A pdb=" N LEU F 307 " --> pdb=" O LEU F 318 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU F 318 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR F 309 " --> pdb=" O TYR F 316 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 315 " --> pdb=" O MET F 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 417 through 418 Processing sheet with id=AA3, first strand: chain 'F' and resid 450 through 452 removed outlier: 3.967A pdb=" N LYS F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE F 441 " --> pdb=" O ILE F 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 25 through 26 Processing sheet with id=AA5, first strand: chain 'D' and resid 96 through 103 removed outlier: 6.041A pdb=" N LEU D 96 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASN D 155 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ILE D 98 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE D 153 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASP D 100 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL D 151 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY D 9 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER D 3 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LYS D 4 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR D 201 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS D 6 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE D 199 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER D 8 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR D 197 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 119 through 124 Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.606A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.606A pdb=" N PHE C 102 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS C 4 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR C 10 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASP C 196 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU C 12 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N PHE C 194 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 119 through 127 Processing sheet with id=AB1, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.715A pdb=" N ALA A 101 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL A 151 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 101 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASP A 149 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE A 103 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLU A 147 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS A 4 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A 10 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASP A 196 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU A 12 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N PHE A 194 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 119 through 126 removed outlier: 3.703A pdb=" N ASN A 135 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.515A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.728A pdb=" N SER B 3 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LYS B 4 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N THR B 201 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS B 6 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE B 199 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER B 8 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR B 197 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 119 through 127 Processing sheet with id=AB6, first strand: chain 'H' and resid 63 through 65 removed outlier: 3.506A pdb=" N GLY H 160 " --> pdb=" O TYR H 65 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL H 7 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE H 203 " --> pdb=" O VAL H 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 58 through 59 Processing sheet with id=AB8, first strand: chain 'H' and resid 71 through 73 Processing sheet with id=AB9, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AC1, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AC2, first strand: chain 'H' and resid 243 through 248 removed outlier: 3.631A pdb=" N SER H 267 " --> pdb=" O THR H 244 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N GLY H 248 " --> pdb=" O SER H 263 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER H 263 " --> pdb=" O GLY H 248 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 283 through 284 704 hydrogen bonds defined for protein. 2040 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 4.36 Time building geometry restraints manager: 4.93 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: 3599 1.33 - 1.45: 3653 1.45 - 1.57: 8282 1.57 - 1.70: 85 1.70 - 1.82: 69 Bond restraints: 15688 Sorted by residual: bond pdb=" O3' A G 13 " pdb=" P A G 14 " ideal model delta sigma weight residual 1.607 1.670 -0.063 1.50e-02 4.44e+03 1.78e+01 bond pdb=" N ILE F 415 " pdb=" CA ILE F 415 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.54e+00 bond pdb=" N GLU B 87 " pdb=" CA GLU B 87 " ideal model delta sigma weight residual 1.458 1.486 -0.028 9.00e-03 1.23e+04 9.47e+00 bond pdb=" N LEU A 130 " pdb=" CA LEU A 130 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.42e+00 bond pdb=" N VAL I 20 " pdb=" CA VAL I 20 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 9.34e+00 ... (remaining 15683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 20974 2.52 - 5.03: 281 5.03 - 7.55: 27 7.55 - 10.07: 1 10.07 - 12.59: 1 Bond angle restraints: 21284 Sorted by residual: angle pdb=" C4' A G 14 " pdb=" C3' A G 14 " pdb=" O3' A G 14 " ideal model delta sigma weight residual 113.00 125.59 -12.59 1.50e+00 4.44e-01 7.04e+01 angle pdb=" O3' A G 14 " pdb=" C3' A G 14 " pdb=" C2' A G 14 " ideal model delta sigma weight residual 113.70 104.36 9.34 1.50e+00 4.44e-01 3.88e+01 angle pdb=" N GLU D 205 " pdb=" CA GLU D 205 " pdb=" C GLU D 205 " ideal model delta sigma weight residual 113.50 107.68 5.82 1.23e+00 6.61e-01 2.24e+01 angle pdb=" N GLU B 87 " pdb=" CA GLU B 87 " pdb=" C GLU B 87 " ideal model delta sigma weight residual 113.50 106.33 7.17 1.65e+00 3.67e-01 1.89e+01 angle pdb=" C4' A G 14 " pdb=" C3' A G 14 " pdb=" C2' A G 14 " ideal model delta sigma weight residual 102.60 98.27 4.33 1.00e+00 1.00e+00 1.87e+01 ... (remaining 21279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 9261 34.94 - 69.87: 172 69.87 - 104.81: 16 104.81 - 139.74: 0 139.74 - 174.68: 3 Dihedral angle restraints: 9452 sinusoidal: 4292 harmonic: 5160 Sorted by residual: dihedral pdb=" O4' C G 28 " pdb=" C1' C G 28 " pdb=" N1 C G 28 " pdb=" C2 C G 28 " ideal model delta sinusoidal sigma weight residual 200.00 43.39 156.61 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual -128.00 46.68 -174.68 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C G 8 " pdb=" C1' C G 8 " pdb=" N1 C G 8 " pdb=" C2 C G 8 " ideal model delta sinusoidal sigma weight residual -160.00 -88.21 -71.79 1 1.50e+01 4.44e-03 2.93e+01 ... (remaining 9449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1666 0.043 - 0.087: 542 0.087 - 0.130: 143 0.130 - 0.174: 22 0.174 - 0.217: 6 Chirality restraints: 2379 Sorted by residual: chirality pdb=" CB ILE F 415 " pdb=" CA ILE F 415 " pdb=" CG1 ILE F 415 " pdb=" CG2 ILE F 415 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C1' U L 8 " pdb=" O4' U L 8 " pdb=" C2' U L 8 " pdb=" N1 U L 8 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA GLU B 87 " pdb=" N GLU B 87 " pdb=" C GLU B 87 " pdb=" CB GLU B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.80e-01 ... (remaining 2376 not shown) Planarity restraints: 2568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A L 16 " -0.043 2.00e-02 2.50e+03 1.86e-02 9.50e+00 pdb=" N9 A L 16 " 0.040 2.00e-02 2.50e+03 pdb=" C8 A L 16 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A L 16 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A L 16 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A L 16 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A L 16 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A L 16 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A L 16 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A L 16 " 0.010 2.00e-02 2.50e+03 pdb=" C4 A L 16 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN J 54 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C GLN J 54 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN J 54 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL J 55 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG I 57 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C ARG I 57 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG I 57 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU I 58 " -0.015 2.00e-02 2.50e+03 ... (remaining 2565 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 4 2.08 - 2.78: 3498 2.78 - 3.49: 20574 3.49 - 4.19: 34226 4.19 - 4.90: 59731 Nonbonded interactions: 118033 Sorted by model distance: nonbonded pdb=" OD1 ASN C 57 " pdb=" NH1 ARG A 129 " model vdw 1.373 3.120 nonbonded pdb=" ND2 ASN B 57 " pdb=" O2 C G 8 " model vdw 1.819 3.120 nonbonded pdb=" OD1 ASN C 57 " pdb=" CZ ARG A 129 " model vdw 1.957 3.270 nonbonded pdb=" OG1 THR C 126 " pdb=" O2' U G 25 " model vdw 2.066 3.040 nonbonded pdb=" ND2 ASN C 57 " pdb=" N7 G G 20 " model vdw 2.117 3.200 ... (remaining 118028 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 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 7)) selection = (chain 'B' and resid 2 through 207) selection = (chain 'C' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 7)) selection = (chain 'D' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 7)) } ncs_group { reference = (chain 'I' and (resid 17 through 61 or resid 74 through 137)) selection = (chain 'J' and (resid 17 through 24 or resid 39 through 137)) } 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 group one per residue 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: 3.200 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: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 38.980 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 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 : 0.005 0.063 15688 Z= 0.329 Angle : 0.756 12.585 21284 Z= 0.461 Chirality : 0.046 0.217 2379 Planarity : 0.005 0.057 2568 Dihedral : 13.953 174.677 6120 Min Nonbonded Distance : 1.373 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.74 % Favored : 95.20 % Rotamer: Outliers : 0.38 % Allowed : 4.04 % Favored : 95.58 % 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: -0.62 (0.19), residues: 1729 helix: 0.42 (0.18), residues: 764 sheet: 0.09 (0.29), residues: 292 loop : -1.58 (0.21), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 184 HIS 0.008 0.001 HIS F 14 PHE 0.016 0.002 PHE A 148 TYR 0.020 0.002 TYR H 200 ARG 0.009 0.001 ARG K 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 431 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 380 LEU cc_start: 0.8314 (tp) cc_final: 0.7670 (pp) REVERT: J 53 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8781 (mm-30) REVERT: I 51 LEU cc_start: 0.9205 (mt) cc_final: 0.8557 (mt) outliers start: 6 outliers final: 0 residues processed: 435 average time/residue: 0.3696 time to fit residues: 212.8469 Evaluate side-chains 201 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 0.0980 chunk 46 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 5 ASN ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN F 83 ASN F 183 GLN F 314 HIS F 397 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN D 189 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN C 110 HIS A 69 GLN A 97 GLN ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15688 Z= 0.229 Angle : 0.657 8.970 21284 Z= 0.351 Chirality : 0.044 0.207 2379 Planarity : 0.004 0.073 2568 Dihedral : 14.869 177.254 2555 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 0.06 % Allowed : 2.90 % Favored : 97.03 % 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: -0.25 (0.19), residues: 1729 helix: 0.75 (0.18), residues: 789 sheet: 0.31 (0.29), residues: 298 loop : -1.54 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 52 HIS 0.013 0.001 HIS C 110 PHE 0.040 0.002 PHE K 85 TYR 0.040 0.002 TYR I 80 ARG 0.007 0.001 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 33 HIS cc_start: 0.6208 (p-80) cc_final: 0.5960 (p-80) REVERT: F 163 MET cc_start: 0.4008 (ptt) cc_final: 0.3223 (ppp) REVERT: J 128 GLU cc_start: 0.7398 (tt0) cc_final: 0.7122 (tt0) REVERT: I 49 ARG cc_start: 0.8505 (pmt170) cc_final: 0.7917 (pmt170) REVERT: I 58 LEU cc_start: 0.9287 (mt) cc_final: 0.8746 (mm) REVERT: I 70 LEU cc_start: 0.7008 (mp) cc_final: 0.6347 (mp) REVERT: I 86 TYR cc_start: 0.8592 (m-80) cc_final: 0.8130 (m-80) REVERT: C 128 ASN cc_start: 0.8474 (t0) cc_final: 0.8198 (t0) REVERT: A 178 ASN cc_start: 0.7908 (t0) cc_final: 0.7687 (t0) REVERT: B 115 ASP cc_start: 0.8562 (m-30) cc_final: 0.8078 (m-30) outliers start: 1 outliers final: 1 residues processed: 254 average time/residue: 0.3291 time to fit residues: 116.8593 Evaluate side-chains 176 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 134 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 144 optimal weight: 0.6980 chunk 160 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 129 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15688 Z= 0.178 Angle : 0.585 10.541 21284 Z= 0.310 Chirality : 0.042 0.340 2379 Planarity : 0.004 0.035 2568 Dihedral : 14.779 176.390 2555 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: -0.15 (0.19), residues: 1729 helix: 0.80 (0.18), residues: 785 sheet: 0.41 (0.29), residues: 300 loop : -1.44 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 52 HIS 0.006 0.001 HIS H 174 PHE 0.029 0.002 PHE K 85 TYR 0.019 0.001 TYR I 87 ARG 0.017 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 33 HIS cc_start: 0.6292 (p-80) cc_final: 0.6045 (p-80) REVERT: J 53 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8214 (mm-30) REVERT: J 109 ASP cc_start: 0.9025 (t0) cc_final: 0.8404 (m-30) REVERT: I 41 ASN cc_start: 0.8621 (m-40) cc_final: 0.8339 (m-40) REVERT: I 49 ARG cc_start: 0.8583 (pmt170) cc_final: 0.8043 (pmt170) REVERT: I 70 LEU cc_start: 0.6709 (mp) cc_final: 0.5730 (mp) REVERT: I 85 PHE cc_start: 0.9090 (m-80) cc_final: 0.8571 (m-80) REVERT: K 86 TYR cc_start: 0.8420 (m-10) cc_final: 0.8086 (m-10) REVERT: K 104 MET cc_start: 0.8218 (ppp) cc_final: 0.7543 (ppp) REVERT: K 105 PHE cc_start: 0.8880 (m-80) cc_final: 0.8494 (m-80) REVERT: C 100 ASP cc_start: 0.7452 (t0) cc_final: 0.6811 (m-30) REVERT: C 128 ASN cc_start: 0.8571 (t0) cc_final: 0.8136 (t0) REVERT: A 144 ARG cc_start: 0.7492 (ptm-80) cc_final: 0.7213 (tmm-80) REVERT: B 115 ASP cc_start: 0.8463 (m-30) cc_final: 0.7987 (m-30) REVERT: H 22 ARG cc_start: 0.7408 (tpm170) cc_final: 0.7204 (mmm160) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2983 time to fit residues: 94.0349 Evaluate side-chains 164 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 17 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 GLN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 HIS B 174 HIS ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15688 Z= 0.254 Angle : 0.631 11.790 21284 Z= 0.332 Chirality : 0.042 0.168 2379 Planarity : 0.004 0.044 2568 Dihedral : 14.976 174.537 2555 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.36 % Rotamer: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % 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: -0.26 (0.19), residues: 1729 helix: 0.71 (0.18), residues: 788 sheet: 0.39 (0.29), residues: 302 loop : -1.54 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 52 HIS 0.005 0.001 HIS F 314 PHE 0.033 0.002 PHE K 85 TYR 0.026 0.002 TYR I 87 ARG 0.004 0.001 ARG I 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.4951 (mmm) cc_final: 0.1395 (ttt) REVERT: F 33 HIS cc_start: 0.6719 (p-80) cc_final: 0.6399 (p-80) REVERT: J 53 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8572 (mm-30) REVERT: J 109 ASP cc_start: 0.9027 (t0) cc_final: 0.8457 (m-30) REVERT: I 41 ASN cc_start: 0.8560 (m-40) cc_final: 0.8333 (m-40) REVERT: I 49 ARG cc_start: 0.8478 (pmt170) cc_final: 0.7871 (pmt170) REVERT: I 70 LEU cc_start: 0.6761 (mp) cc_final: 0.5524 (mp) REVERT: I 85 PHE cc_start: 0.9223 (m-80) cc_final: 0.8927 (m-80) REVERT: K 104 MET cc_start: 0.8357 (ppp) cc_final: 0.7897 (ppp) REVERT: K 105 PHE cc_start: 0.8780 (m-80) cc_final: 0.8315 (m-80) REVERT: C 100 ASP cc_start: 0.7469 (t0) cc_final: 0.6965 (m-30) REVERT: C 128 ASN cc_start: 0.8582 (t0) cc_final: 0.8238 (t0) REVERT: A 55 MET cc_start: 0.6272 (mmm) cc_final: 0.5999 (mmt) REVERT: A 144 ARG cc_start: 0.7648 (ptm-80) cc_final: 0.7283 (tmm-80) REVERT: B 168 ASN cc_start: 0.8464 (m110) cc_final: 0.8219 (m110) REVERT: H 22 ARG cc_start: 0.7647 (tpm170) cc_final: 0.7259 (mmm160) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.2821 time to fit residues: 82.4189 Evaluate side-chains 146 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 154 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS D 62 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15688 Z= 0.207 Angle : 0.589 12.144 21284 Z= 0.310 Chirality : 0.041 0.177 2379 Planarity : 0.004 0.044 2568 Dihedral : 15.048 176.596 2555 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.59 % Rotamer: Outliers : 0.06 % Allowed : 2.15 % Favored : 97.79 % 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: -0.23 (0.19), residues: 1729 helix: 0.71 (0.18), residues: 796 sheet: 0.31 (0.29), residues: 299 loop : -1.45 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 52 HIS 0.013 0.001 HIS F 26 PHE 0.030 0.002 PHE K 85 TYR 0.034 0.002 TYR K 86 ARG 0.005 0.001 ARG K 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 33 HIS cc_start: 0.6888 (p-80) cc_final: 0.6540 (p-80) REVERT: F 452 MET cc_start: 0.3156 (mmp) cc_final: 0.2507 (mmm) REVERT: J 53 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8583 (mm-30) REVERT: J 109 ASP cc_start: 0.9051 (t0) cc_final: 0.8475 (m-30) REVERT: I 41 ASN cc_start: 0.8535 (m-40) cc_final: 0.8331 (m-40) REVERT: I 70 LEU cc_start: 0.6608 (mp) cc_final: 0.6367 (mp) REVERT: I 85 PHE cc_start: 0.9099 (m-80) cc_final: 0.8811 (m-80) REVERT: K 104 MET cc_start: 0.8614 (ppp) cc_final: 0.8061 (ppp) REVERT: K 105 PHE cc_start: 0.8775 (m-80) cc_final: 0.8420 (m-80) REVERT: C 67 MET cc_start: 0.7873 (tmm) cc_final: 0.7567 (tmm) REVERT: C 100 ASP cc_start: 0.7516 (t0) cc_final: 0.6969 (m-30) REVERT: C 128 ASN cc_start: 0.8621 (t0) cc_final: 0.8308 (t0) REVERT: B 115 ASP cc_start: 0.7931 (m-30) cc_final: 0.7657 (m-30) REVERT: B 168 ASN cc_start: 0.8556 (m110) cc_final: 0.8320 (m110) REVERT: B 181 LEU cc_start: 0.8764 (tp) cc_final: 0.8530 (tp) REVERT: H 22 ARG cc_start: 0.7318 (tpm170) cc_final: 0.6988 (mmm160) outliers start: 1 outliers final: 1 residues processed: 193 average time/residue: 0.2882 time to fit residues: 81.7860 Evaluate side-chains 139 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN H 87 HIS H 122 ASN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.6718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15688 Z= 0.267 Angle : 0.657 11.518 21284 Z= 0.348 Chirality : 0.043 0.284 2379 Planarity : 0.004 0.050 2568 Dihedral : 15.327 174.069 2555 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: -0.53 (0.19), residues: 1729 helix: 0.44 (0.18), residues: 788 sheet: 0.08 (0.29), residues: 303 loop : -1.51 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 52 HIS 0.007 0.001 HIS F 26 PHE 0.036 0.002 PHE H 163 TYR 0.019 0.002 TYR J 133 ARG 0.008 0.001 ARG I 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 53 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8556 (mm-30) REVERT: J 109 ASP cc_start: 0.9036 (t0) cc_final: 0.8489 (m-30) REVERT: I 41 ASN cc_start: 0.8578 (m-40) cc_final: 0.8366 (m-40) REVERT: I 70 LEU cc_start: 0.6687 (mp) cc_final: 0.5788 (mp) REVERT: I 85 PHE cc_start: 0.9151 (m-80) cc_final: 0.8820 (m-80) REVERT: I 128 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8606 (mm-30) REVERT: I 133 TYR cc_start: 0.8345 (m-80) cc_final: 0.7701 (m-80) REVERT: K 86 TYR cc_start: 0.8637 (m-80) cc_final: 0.8343 (m-80) REVERT: K 104 MET cc_start: 0.8595 (ppp) cc_final: 0.8052 (ppp) REVERT: D 90 ASN cc_start: 0.8308 (p0) cc_final: 0.7151 (p0) REVERT: C 100 ASP cc_start: 0.7613 (t0) cc_final: 0.7290 (m-30) REVERT: C 128 ASN cc_start: 0.8555 (t0) cc_final: 0.8107 (t0) REVERT: B 168 ASN cc_start: 0.8639 (m110) cc_final: 0.8413 (m110) REVERT: B 181 LEU cc_start: 0.8876 (tp) cc_final: 0.8646 (tp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2812 time to fit residues: 77.7226 Evaluate side-chains 140 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 125 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 171 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.6902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15688 Z= 0.166 Angle : 0.581 14.035 21284 Z= 0.302 Chirality : 0.041 0.152 2379 Planarity : 0.004 0.054 2568 Dihedral : 15.248 177.106 2555 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -0.16 (0.19), residues: 1729 helix: 0.81 (0.18), residues: 790 sheet: 0.22 (0.29), residues: 301 loop : -1.41 (0.22), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 52 HIS 0.007 0.001 HIS D 110 PHE 0.027 0.002 PHE K 85 TYR 0.017 0.001 TYR I 87 ARG 0.011 0.001 ARG I 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 66 LYS cc_start: 0.8683 (mptt) cc_final: 0.8447 (mppt) REVERT: F 452 MET cc_start: 0.2985 (mmp) cc_final: 0.2308 (mmm) REVERT: J 53 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8528 (mm-30) REVERT: J 109 ASP cc_start: 0.9009 (t0) cc_final: 0.8469 (m-30) REVERT: I 85 PHE cc_start: 0.9140 (m-80) cc_final: 0.8862 (m-80) REVERT: I 104 MET cc_start: 0.8044 (tmm) cc_final: 0.7575 (tmm) REVERT: I 128 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8532 (mm-30) REVERT: I 133 TYR cc_start: 0.8314 (m-80) cc_final: 0.7643 (m-80) REVERT: K 86 TYR cc_start: 0.8608 (m-80) cc_final: 0.8360 (m-80) REVERT: D 54 LYS cc_start: 0.8254 (mmtt) cc_final: 0.8039 (mmtt) REVERT: C 100 ASP cc_start: 0.7293 (t0) cc_final: 0.7012 (m-30) REVERT: C 128 ASN cc_start: 0.8572 (t0) cc_final: 0.8253 (t0) REVERT: A 116 ILE cc_start: 0.7654 (mt) cc_final: 0.7312 (mt) REVERT: B 115 ASP cc_start: 0.7876 (m-30) cc_final: 0.7631 (m-30) REVERT: B 168 ASN cc_start: 0.8585 (m110) cc_final: 0.8301 (m-40) REVERT: B 181 LEU cc_start: 0.8852 (tp) cc_final: 0.8622 (tp) REVERT: H 226 MET cc_start: 0.6285 (mmm) cc_final: 0.6049 (mmt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2702 time to fit residues: 75.1035 Evaluate side-chains 140 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 0.0020 chunk 109 optimal weight: 0.5980 chunk 116 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 156 optimal weight: 0.4980 chunk 164 optimal weight: 3.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.6999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15688 Z= 0.146 Angle : 0.564 12.756 21284 Z= 0.292 Chirality : 0.041 0.148 2379 Planarity : 0.003 0.041 2568 Dihedral : 15.201 176.714 2555 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 0.01 (0.19), residues: 1729 helix: 0.99 (0.18), residues: 785 sheet: 0.21 (0.29), residues: 297 loop : -1.28 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 52 HIS 0.007 0.001 HIS H 17 PHE 0.026 0.001 PHE K 85 TYR 0.015 0.001 TYR I 87 ARG 0.006 0.000 ARG I 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.5097 (mmm) cc_final: 0.1167 (ttt) REVERT: F 66 LYS cc_start: 0.8680 (mptt) cc_final: 0.8450 (mppt) REVERT: J 53 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8414 (mm-30) REVERT: J 109 ASP cc_start: 0.8945 (t0) cc_final: 0.8414 (m-30) REVERT: J 112 ILE cc_start: 0.8568 (pt) cc_final: 0.8243 (pt) REVERT: I 85 PHE cc_start: 0.9107 (m-80) cc_final: 0.8859 (m-80) REVERT: I 104 MET cc_start: 0.7948 (tmm) cc_final: 0.7429 (tmm) REVERT: I 128 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8582 (mm-30) REVERT: I 133 TYR cc_start: 0.8191 (m-80) cc_final: 0.7569 (m-80) REVERT: K 86 TYR cc_start: 0.8556 (m-80) cc_final: 0.8356 (m-80) REVERT: K 104 MET cc_start: 0.8852 (ppp) cc_final: 0.8388 (ppp) REVERT: C 128 ASN cc_start: 0.8639 (t0) cc_final: 0.8329 (t0) REVERT: A 116 ILE cc_start: 0.7400 (mt) cc_final: 0.7019 (mt) REVERT: B 115 ASP cc_start: 0.7869 (m-30) cc_final: 0.7605 (m-30) REVERT: B 168 ASN cc_start: 0.8509 (m110) cc_final: 0.8226 (m-40) REVERT: B 181 LEU cc_start: 0.8814 (tp) cc_final: 0.8595 (tp) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2640 time to fit residues: 74.6630 Evaluate side-chains 136 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 164 optimal weight: 0.0070 chunk 96 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 49 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN B 178 ASN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.7176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15688 Z= 0.154 Angle : 0.577 12.615 21284 Z= 0.301 Chirality : 0.041 0.166 2379 Planarity : 0.003 0.043 2568 Dihedral : 15.187 176.804 2555 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 0.06 (0.19), residues: 1729 helix: 1.00 (0.18), residues: 789 sheet: 0.29 (0.29), residues: 303 loop : -1.26 (0.22), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 52 HIS 0.006 0.001 HIS D 110 PHE 0.025 0.001 PHE K 85 TYR 0.018 0.001 TYR I 87 ARG 0.006 0.000 ARG K 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.5023 (mmm) cc_final: 0.1214 (ttt) REVERT: F 66 LYS cc_start: 0.8685 (mptt) cc_final: 0.8459 (mppt) REVERT: J 53 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8423 (mm-30) REVERT: J 109 ASP cc_start: 0.8928 (t0) cc_final: 0.8439 (m-30) REVERT: J 112 ILE cc_start: 0.8555 (pt) cc_final: 0.8228 (pt) REVERT: I 85 PHE cc_start: 0.8956 (m-80) cc_final: 0.8706 (m-80) REVERT: I 104 MET cc_start: 0.7832 (tmm) cc_final: 0.7278 (tmm) REVERT: I 133 TYR cc_start: 0.8163 (m-80) cc_final: 0.7556 (m-80) REVERT: C 128 ASN cc_start: 0.8696 (t0) cc_final: 0.8393 (t0) REVERT: B 115 ASP cc_start: 0.7917 (m-30) cc_final: 0.7662 (m-30) REVERT: B 168 ASN cc_start: 0.8497 (m110) cc_final: 0.8253 (m110) REVERT: B 181 LEU cc_start: 0.8850 (tp) cc_final: 0.8644 (tp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2817 time to fit residues: 76.6950 Evaluate side-chains 133 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 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 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN D 189 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.7495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15688 Z= 0.214 Angle : 0.609 11.906 21284 Z= 0.323 Chirality : 0.041 0.156 2379 Planarity : 0.004 0.047 2568 Dihedral : 15.356 174.739 2555 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -0.12 (0.19), residues: 1729 helix: 0.81 (0.18), residues: 789 sheet: 0.13 (0.29), residues: 305 loop : -1.27 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 52 HIS 0.005 0.001 HIS D 110 PHE 0.020 0.002 PHE H 153 TYR 0.020 0.002 TYR I 87 ARG 0.005 0.001 ARG I 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 363 MET cc_start: -0.1485 (tpt) cc_final: -0.1774 (tpt) REVERT: J 53 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8419 (mm-30) REVERT: J 109 ASP cc_start: 0.8966 (t0) cc_final: 0.8498 (m-30) REVERT: J 122 ASP cc_start: 0.9082 (m-30) cc_final: 0.8873 (m-30) REVERT: J 127 PHE cc_start: 0.8621 (t80) cc_final: 0.8309 (t80) REVERT: I 85 PHE cc_start: 0.8983 (m-80) cc_final: 0.8690 (m-80) REVERT: I 104 MET cc_start: 0.7793 (tmm) cc_final: 0.7285 (tmm) REVERT: I 133 TYR cc_start: 0.8121 (m-80) cc_final: 0.7643 (m-80) REVERT: K 85 PHE cc_start: 0.8720 (m-10) cc_final: 0.8412 (m-80) REVERT: K 104 MET cc_start: 0.8786 (ppp) cc_final: 0.8267 (ppp) REVERT: C 128 ASN cc_start: 0.8751 (t0) cc_final: 0.8443 (t0) REVERT: A 52 LYS cc_start: 0.6266 (tttm) cc_final: 0.6013 (tttt) REVERT: A 144 ARG cc_start: 0.7955 (ptm160) cc_final: 0.7650 (ptm-80) REVERT: A 207 ASP cc_start: 0.8354 (m-30) cc_final: 0.8113 (p0) REVERT: B 115 ASP cc_start: 0.7810 (m-30) cc_final: 0.7530 (m-30) REVERT: B 168 ASN cc_start: 0.8664 (m110) cc_final: 0.8454 (m110) REVERT: B 181 LEU cc_start: 0.8902 (tp) cc_final: 0.8621 (tt) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2559 time to fit residues: 66.2762 Evaluate side-chains 130 residues out of total 1584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 HIS ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.064627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.053693 restraints weight = 148015.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.055009 restraints weight = 101442.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.055813 restraints weight = 74942.613| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.7626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15688 Z= 0.170 Angle : 0.588 12.898 21284 Z= 0.308 Chirality : 0.041 0.158 2379 Planarity : 0.004 0.044 2568 Dihedral : 15.319 176.768 2555 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.19), residues: 1729 helix: 0.81 (0.18), residues: 791 sheet: 0.17 (0.29), residues: 303 loop : -1.28 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 52 HIS 0.006 0.001 HIS D 110 PHE 0.039 0.001 PHE J 85 TYR 0.049 0.001 TYR K 86 ARG 0.005 0.001 ARG I 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3138.66 seconds wall clock time: 57 minutes 22.64 seconds (3442.64 seconds total)