Starting phenix.real_space_refine on Tue Nov 19 00:01:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcu_15968/11_2024/8bcu_15968.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcu_15968/11_2024/8bcu_15968.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/8bcu_15968/11_2024/8bcu_15968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcu_15968/11_2024/8bcu_15968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcu_15968/11_2024/8bcu_15968.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bcu_15968/11_2024/8bcu_15968.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= 0.002 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 11475 2.51 5 N 3051 2.21 5 O 3687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18279 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1279 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 150} Chain: "D" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 149} Chain: "H" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "A" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1279 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 150} Chain: "B" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 149} Chain: "G" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Chain: "E" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1279 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 150} Chain: "F" Number of atoms: 1268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1268 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 149} Chain: "I" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3546 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 449} Time building chain proxies: 10.60, per 1000 atoms: 0.58 Number of scatterers: 18279 At special positions: 0 Unit cell: (154.014, 163.471, 104.027, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 3687 8.00 N 3051 7.00 C 11475 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.43 Conformation dependent library (CDL) restraints added in 2.5 seconds 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 30 sheets defined 16.5% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 85 through 103 Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 41 through 45 Processing helix chain 'D' and resid 85 through 103 Processing helix chain 'H' and resid 5 through 7 No H-bonds generated for 'chain 'H' and resid 5 through 7' Processing helix chain 'H' and resid 91 through 100 Processing helix chain 'H' and resid 185 through 190 Processing helix chain 'H' and resid 192 through 201 removed outlier: 4.083A pdb=" N GLY H 201 " --> pdb=" O MET H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 287 removed outlier: 3.523A pdb=" N LEU H 287 " --> pdb=" O LEU H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 369 Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 85 through 103 Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 85 through 103 Processing helix chain 'G' and resid 5 through 7 No H-bonds generated for 'chain 'G' and resid 5 through 7' Processing helix chain 'G' and resid 91 through 100 Processing helix chain 'G' and resid 185 through 190 Processing helix chain 'G' and resid 192 through 201 removed outlier: 4.325A pdb=" N GLY G 201 " --> pdb=" O MET G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 287 Processing helix chain 'G' and resid 358 through 369 Processing helix chain 'E' and resid 3 through 18 Processing helix chain 'E' and resid 85 through 103 Processing helix chain 'F' and resid 3 through 18 Processing helix chain 'F' and resid 41 through 45 Processing helix chain 'F' and resid 85 through 103 Processing helix chain 'I' and resid 5 through 7 No H-bonds generated for 'chain 'I' and resid 5 through 7' Processing helix chain 'I' and resid 91 through 100 Processing helix chain 'I' and resid 185 through 190 Processing helix chain 'I' and resid 192 through 201 removed outlier: 4.165A pdb=" N GLY I 201 " --> pdb=" O MET I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 275 through 287 Processing helix chain 'I' and resid 358 through 369 Processing sheet with id=AA1, first strand: chain 'C' and resid 35 through 36 removed outlier: 7.007A pdb=" N SER C 36 " --> pdb=" O VAL C 53 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 50 through 53 current: chain 'C' and resid 70 through 73 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 70 through 73 current: chain 'C' and resid 141 through 152 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 141 through 152 current: chain 'D' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 50 through 53 current: chain 'D' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 68 through 72 current: chain 'D' and resid 141 through 148 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 141 through 148 current: chain 'A' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 50 through 53 current: chain 'A' and resid 68 through 73 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 68 through 73 current: chain 'A' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 144 through 152 current: chain 'B' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 50 through 53 current: chain 'B' and resid 68 through 81 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 68 through 81 current: chain 'B' and resid 141 through 152 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 141 through 152 current: chain 'E' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 50 through 53 current: chain 'E' and resid 68 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 68 through 73 current: chain 'E' and resid 144 through 152 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 144 through 152 current: chain 'F' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 50 through 53 current: chain 'F' and resid 68 through 81 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 68 through 81 current: chain 'F' and resid 141 through 152 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 108 through 112 Processing sheet with id=AA3, first strand: chain 'D' and resid 109 through 111 Processing sheet with id=AA4, first strand: chain 'H' and resid 25 through 28 removed outlier: 4.314A pdb=" N ILE H 11 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER H 14 " --> pdb=" O HIS H 135 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP H 144 " --> pdb=" O LEU H 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 35 through 37 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 68 through 71 current: chain 'H' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 119 through 122 current: chain 'H' and resid 166 through 173 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 166 through 173 current: chain 'H' and resid 220 through 224 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 220 through 224 current: chain 'H' and resid 261 through 268 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 261 through 268 current: chain 'H' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 307 through 319 current: chain 'H' and resid 331 through 338 Processing sheet with id=AA6, first strand: chain 'H' and resid 43 through 46 Processing sheet with id=AA7, first strand: chain 'H' and resid 79 through 81 removed outlier: 3.735A pdb=" N LYS H 86 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 378 through 382 removed outlier: 3.517A pdb=" N THR H 380 " --> pdb=" O GLU H 401 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 389 through 391 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 389 through 391 current: chain 'H' and resid 440 through 446 removed outlier: 3.936A pdb=" N ALA H 444 " --> pdb=" O GLY H 454 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY H 454 " --> pdb=" O ALA H 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 395 through 396 Processing sheet with id=AB2, first strand: chain 'A' and resid 108 through 112 Processing sheet with id=AB3, first strand: chain 'B' and resid 108 through 111 Processing sheet with id=AB4, first strand: chain 'G' and resid 25 through 28 removed outlier: 4.368A pdb=" N ILE G 11 " --> pdb=" O ILE G 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE G 136 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP G 144 " --> pdb=" O LEU G 179 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 35 through 37 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 68 through 75 current: chain 'G' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 119 through 122 current: chain 'G' and resid 166 through 173 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 166 through 173 current: chain 'G' and resid 220 through 234 removed outlier: 7.818A pdb=" N ILE G 226 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR G 268 " --> pdb=" O ILE G 226 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY G 228 " --> pdb=" O THR G 266 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 261 through 268 current: chain 'G' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 307 through 319 current: chain 'G' and resid 331 through 338 Processing sheet with id=AB6, first strand: chain 'G' and resid 43 through 46 Processing sheet with id=AB7, first strand: chain 'G' and resid 79 through 81 removed outlier: 3.782A pdb=" N LYS G 86 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 238 through 240 removed outlier: 3.842A pdb=" N GLY G 253 " --> pdb=" O LEU G 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 378 through 382 removed outlier: 3.612A pdb=" N GLU G 401 " --> pdb=" O THR G 380 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 389 through 391 removed outlier: 7.071A pdb=" N LEU G 390 " --> pdb=" O THR G 461 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR G 441 " --> pdb=" O THR G 417 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 395 through 396 Processing sheet with id=AC3, first strand: chain 'E' and resid 108 through 112 Processing sheet with id=AC4, first strand: chain 'F' and resid 108 through 111 Processing sheet with id=AC5, first strand: chain 'I' and resid 25 through 28 removed outlier: 4.370A pdb=" N ILE I 11 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TRP I 144 " --> pdb=" O LEU I 179 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 35 through 37 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 68 through 71 current: chain 'I' and resid 119 through 122 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 119 through 122 current: chain 'I' and resid 166 through 173 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 166 through 173 current: chain 'I' and resid 220 through 224 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 220 through 224 current: chain 'I' and resid 261 through 268 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 261 through 268 current: chain 'I' and resid 307 through 319 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 307 through 319 current: chain 'I' and resid 331 through 338 Processing sheet with id=AC7, first strand: chain 'I' and resid 43 through 46 Processing sheet with id=AC8, first strand: chain 'I' and resid 79 through 80 Processing sheet with id=AC9, first strand: chain 'I' and resid 238 through 240 removed outlier: 3.514A pdb=" N GLY I 253 " --> pdb=" O LEU I 240 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 378 through 382 Processing sheet with id=AD2, first strand: chain 'I' and resid 389 through 390 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 389 through 390 current: chain 'I' and resid 440 through 446 removed outlier: 3.943A pdb=" N ALA I 444 " --> pdb=" O GLY I 454 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY I 454 " --> pdb=" O ALA I 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 395 through 397 411 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6087 1.34 - 1.46: 3797 1.46 - 1.58: 8602 1.58 - 1.69: 0 1.69 - 1.81: 123 Bond restraints: 18609 Sorted by residual: bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N MET I 1 " pdb=" CA MET I 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 18604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 23775 1.02 - 2.05: 1282 2.05 - 3.07: 134 3.07 - 4.09: 92 4.09 - 5.12: 19 Bond angle restraints: 25302 Sorted by residual: angle pdb=" N ASN G 368 " pdb=" CA ASN G 368 " pdb=" C ASN G 368 " ideal model delta sigma weight residual 114.56 110.96 3.60 1.27e+00 6.20e-01 8.04e+00 angle pdb=" CA GLU I 194 " pdb=" CB GLU I 194 " pdb=" CG GLU I 194 " ideal model delta sigma weight residual 114.10 119.05 -4.95 2.00e+00 2.50e-01 6.13e+00 angle pdb=" CB GLU I 194 " pdb=" CG GLU I 194 " pdb=" CD GLU I 194 " ideal model delta sigma weight residual 112.60 116.23 -3.63 1.70e+00 3.46e-01 4.55e+00 angle pdb=" N GLY I 229 " pdb=" CA GLY I 229 " pdb=" C GLY I 229 " ideal model delta sigma weight residual 110.38 113.50 -3.12 1.48e+00 4.57e-01 4.45e+00 angle pdb=" CA ASN G 368 " pdb=" C ASN G 368 " pdb=" N GLY G 369 " ideal model delta sigma weight residual 119.26 116.91 2.35 1.14e+00 7.69e-01 4.25e+00 ... (remaining 25297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9669 17.97 - 35.93: 1171 35.93 - 53.90: 291 53.90 - 71.87: 63 71.87 - 89.84: 17 Dihedral angle restraints: 11211 sinusoidal: 4404 harmonic: 6807 Sorted by residual: dihedral pdb=" CA ALA H 310 " pdb=" C ALA H 310 " pdb=" N ILE H 311 " pdb=" CA ILE H 311 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ILE I 226 " pdb=" C ILE I 226 " pdb=" N THR I 227 " pdb=" CA THR I 227 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA PHE D 28 " pdb=" C PHE D 28 " pdb=" N ASN D 29 " pdb=" CA ASN D 29 " ideal model delta harmonic sigma weight residual -180.00 -163.63 -16.37 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 11208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1873 0.033 - 0.065: 717 0.065 - 0.098: 176 0.098 - 0.131: 156 0.131 - 0.163: 12 Chirality restraints: 2934 Sorted by residual: chirality pdb=" CA ILE I 250 " pdb=" N ILE I 250 " pdb=" C ILE I 250 " pdb=" CB ILE I 250 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CA ILE I 177 " pdb=" N ILE I 177 " pdb=" C ILE I 177 " pdb=" CB ILE I 177 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE G 250 " pdb=" N ILE G 250 " pdb=" C ILE G 250 " pdb=" CB ILE G 250 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 2931 not shown) Planarity restraints: 3282 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS F 113 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO F 114 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO F 114 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 114 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 113 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO B 114 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 114 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 114 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 113 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO D 114 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 114 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 114 " 0.018 5.00e-02 4.00e+02 ... (remaining 3279 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 296 2.54 - 3.13: 15757 3.13 - 3.72: 27998 3.72 - 4.31: 38317 4.31 - 4.90: 64941 Nonbonded interactions: 147309 Sorted by model distance: nonbonded pdb=" OG1 THR H 413 " pdb=" OG1 THR H 445 " model vdw 1.950 3.040 nonbonded pdb=" OG1 THR G 413 " pdb=" OG1 THR G 445 " model vdw 1.989 3.040 nonbonded pdb=" OG1 THR H 380 " pdb=" OE2 GLU H 401 " model vdw 1.996 3.040 nonbonded pdb=" OG SER I 14 " pdb=" OG1 THR I 25 " model vdw 2.017 3.040 nonbonded pdb=" NH2 ARG E 14 " pdb=" O VAL E 100 " model vdw 2.069 3.120 ... (remaining 147304 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 1 through 159) selection = chain 'B' selection = (chain 'C' and resid 1 through 159) selection = chain 'D' selection = (chain 'E' and resid 1 through 159) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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=0.00 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: 0.140 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 38.950 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 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 : 0.004 0.034 18609 Z= 0.279 Angle : 0.554 5.118 25302 Z= 0.303 Chirality : 0.043 0.163 2934 Planarity : 0.003 0.039 3282 Dihedral : 16.797 89.836 6843 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.61 % Favored : 93.26 % Rotamer: Outliers : 0.15 % Allowed : 25.43 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 (0.17), residues: 2331 helix: 1.21 (0.29), residues: 324 sheet: -0.16 (0.18), residues: 852 loop : -1.45 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 144 HIS 0.003 0.001 HIS H 129 PHE 0.009 0.001 PHE G 231 TYR 0.015 0.001 TYR G 92 ARG 0.004 0.000 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 682 time to evaluate : 2.126 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: C 96 ASP cc_start: 0.5121 (OUTLIER) cc_final: 0.4670 (t0) REVERT: C 99 THR cc_start: 0.7302 (p) cc_final: 0.6568 (p) REVERT: C 102 ASP cc_start: 0.7821 (m-30) cc_final: 0.7481 (m-30) REVERT: D 16 SER cc_start: 0.7814 (m) cc_final: 0.7332 (p) REVERT: D 34 ASN cc_start: 0.6970 (t0) cc_final: 0.6597 (p0) REVERT: D 128 ILE cc_start: 0.7967 (mt) cc_final: 0.7644 (tp) REVERT: D 159 LEU cc_start: 0.5331 (mt) cc_final: 0.4536 (pp) REVERT: H 191 ILE cc_start: 0.6578 (pt) cc_final: 0.6207 (pt) REVERT: H 210 ILE cc_start: 0.7184 (mt) cc_final: 0.6968 (mt) REVERT: H 224 ILE cc_start: 0.8124 (mm) cc_final: 0.7855 (mp) REVERT: H 226 ILE cc_start: 0.7409 (mt) cc_final: 0.7091 (mt) REVERT: H 236 ASN cc_start: 0.5396 (m-40) cc_final: 0.3484 (m110) REVERT: A 11 MET cc_start: 0.9059 (tpp) cc_final: 0.8683 (ttt) REVERT: A 107 LEU cc_start: 0.8065 (tp) cc_final: 0.7799 (tp) REVERT: B 63 LEU cc_start: 0.8377 (mt) cc_final: 0.8172 (mm) REVERT: B 69 TRP cc_start: 0.7452 (m100) cc_final: 0.7169 (m100) REVERT: B 94 VAL cc_start: 0.7123 (p) cc_final: 0.6910 (p) REVERT: B 153 GLN cc_start: 0.8337 (tt0) cc_final: 0.7866 (tt0) REVERT: G 47 VAL cc_start: 0.8007 (m) cc_final: 0.7752 (p) REVERT: G 73 SER cc_start: 0.7676 (m) cc_final: 0.7422 (t) REVERT: G 122 ASN cc_start: 0.7843 (t0) cc_final: 0.7089 (t0) REVERT: G 144 TRP cc_start: 0.7585 (m100) cc_final: 0.7288 (m100) REVERT: G 213 ILE cc_start: 0.8155 (tt) cc_final: 0.7864 (tt) REVERT: G 264 SER cc_start: 0.7625 (p) cc_final: 0.6982 (t) REVERT: G 280 TYR cc_start: 0.7375 (t80) cc_final: 0.6654 (t80) REVERT: G 333 SER cc_start: 0.6109 (t) cc_final: 0.5861 (t) REVERT: G 398 MET cc_start: 0.4380 (tmm) cc_final: 0.3557 (tmm) REVERT: E 17 LYS cc_start: 0.7836 (ptpt) cc_final: 0.7075 (mmmm) REVERT: E 63 LEU cc_start: 0.7139 (mm) cc_final: 0.6928 (mp) REVERT: E 72 LEU cc_start: 0.7029 (tt) cc_final: 0.6821 (tp) REVERT: F 27 TYR cc_start: 0.7589 (m-10) cc_final: 0.7097 (m-10) REVERT: F 58 GLU cc_start: 0.6517 (tt0) cc_final: 0.6085 (mt-10) REVERT: F 62 TYR cc_start: 0.6646 (m-10) cc_final: 0.6355 (m-10) REVERT: F 72 LEU cc_start: 0.8068 (tp) cc_final: 0.7501 (tp) REVERT: F 86 ILE cc_start: 0.8282 (tt) cc_final: 0.7848 (tt) REVERT: I 24 ASN cc_start: 0.6562 (p0) cc_final: 0.6288 (p0) REVERT: I 294 GLU cc_start: 0.3253 (pt0) cc_final: 0.2440 (pt0) REVERT: I 311 ILE cc_start: 0.5593 (mm) cc_final: 0.5287 (tp) REVERT: I 339 ILE cc_start: 0.8749 (pt) cc_final: 0.8146 (pt) outliers start: 3 outliers final: 1 residues processed: 682 average time/residue: 0.3110 time to fit residues: 319.6128 Evaluate side-chains 400 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 398 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 8.9990 chunk 175 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN C 68 GLN ** D 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 147 ASN H 66 ASN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 106 ASN G 48 ASN G 200 GLN ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS E 68 GLN F 3 HIS ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN I 151 GLN I 153 ASN I 409 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 18609 Z= 0.367 Angle : 0.772 12.070 25302 Z= 0.407 Chirality : 0.052 0.238 2934 Planarity : 0.006 0.078 3282 Dihedral : 4.858 20.520 2529 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.47 % Favored : 96.40 % Rotamer: Outliers : 0.34 % Allowed : 7.46 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.98 (0.17), residues: 2331 helix: 0.23 (0.26), residues: 327 sheet: -0.06 (0.18), residues: 834 loop : -1.34 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 69 HIS 0.013 0.003 HIS B 3 PHE 0.036 0.003 PHE F 119 TYR 0.031 0.003 TYR H 239 ARG 0.012 0.001 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 515 time to evaluate : 2.078 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: C 58 GLU cc_start: 0.7567 (pt0) cc_final: 0.7019 (pt0) REVERT: C 76 ILE cc_start: 0.8966 (mt) cc_final: 0.8707 (mm) REVERT: C 99 THR cc_start: 0.6939 (p) cc_final: 0.6730 (p) REVERT: D 27 TYR cc_start: 0.5450 (m-10) cc_final: 0.5106 (m-10) REVERT: D 99 THR cc_start: 0.8398 (m) cc_final: 0.7526 (t) REVERT: D 159 LEU cc_start: 0.5404 (mt) cc_final: 0.4779 (pp) REVERT: H 129 HIS cc_start: 0.6396 (m-70) cc_final: 0.6112 (m-70) REVERT: H 282 ASP cc_start: 0.7221 (m-30) cc_final: 0.7005 (m-30) REVERT: A 2 ASP cc_start: 0.6440 (t70) cc_final: 0.5800 (t70) REVERT: A 80 ASP cc_start: 0.7171 (t0) cc_final: 0.6820 (t0) REVERT: A 107 LEU cc_start: 0.8462 (tp) cc_final: 0.8240 (tp) REVERT: A 151 ARG cc_start: 0.8206 (ttt-90) cc_final: 0.7757 (ttt-90) REVERT: B 113 LYS cc_start: 0.7876 (mmmt) cc_final: 0.7667 (mmmt) REVERT: G 47 VAL cc_start: 0.8332 (m) cc_final: 0.8057 (p) REVERT: G 120 MET cc_start: 0.8078 (ptp) cc_final: 0.7798 (ptp) REVERT: G 213 ILE cc_start: 0.8841 (tt) cc_final: 0.8537 (tt) REVERT: G 216 MET cc_start: 0.7920 (mmm) cc_final: 0.7150 (mmp) REVERT: G 280 TYR cc_start: 0.7877 (t80) cc_final: 0.7456 (t80) REVERT: G 287 LEU cc_start: 0.8218 (mt) cc_final: 0.7925 (mp) REVERT: G 295 ILE cc_start: 0.8620 (tp) cc_final: 0.8408 (tt) REVERT: G 353 PHE cc_start: 0.8250 (m-80) cc_final: 0.8018 (m-80) REVERT: G 370 ASP cc_start: 0.7296 (t70) cc_final: 0.6956 (t0) REVERT: E 1 MET cc_start: 0.6620 (pmm) cc_final: 0.4741 (tpt) REVERT: E 16 SER cc_start: 0.8485 (t) cc_final: 0.8274 (t) REVERT: F 23 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8209 (mm-40) REVERT: F 85 ASP cc_start: 0.7374 (t0) cc_final: 0.7003 (t70) REVERT: F 126 MET cc_start: 0.6726 (ttm) cc_final: 0.6399 (ttm) REVERT: F 132 SER cc_start: 0.7546 (t) cc_final: 0.6159 (t) REVERT: F 145 GLU cc_start: 0.8163 (pm20) cc_final: 0.7668 (pm20) REVERT: I 246 SER cc_start: 0.8222 (m) cc_final: 0.7701 (p) REVERT: I 342 ASP cc_start: 0.7532 (m-30) cc_final: 0.7308 (t70) REVERT: I 398 MET cc_start: 0.4615 (pmm) cc_final: 0.4389 (pmm) outliers start: 7 outliers final: 0 residues processed: 521 average time/residue: 0.2810 time to fit residues: 227.2771 Evaluate side-chains 337 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 227 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 168 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN D 89 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 ASN H 206 ASN H 363 ASN A 54 HIS ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 ASN G 158 ASN G 174 ASN ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 GLN ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18609 Z= 0.269 Angle : 0.625 8.418 25302 Z= 0.330 Chirality : 0.047 0.219 2934 Planarity : 0.004 0.040 3282 Dihedral : 4.503 19.853 2529 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.44 % Rotamer: Outliers : 0.15 % Allowed : 4.81 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.91 (0.17), residues: 2331 helix: 0.31 (0.26), residues: 333 sheet: -0.23 (0.18), residues: 831 loop : -1.11 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 69 HIS 0.010 0.002 HIS F 3 PHE 0.026 0.002 PHE I 72 TYR 0.022 0.002 TYR I 357 ARG 0.008 0.001 ARG E 4 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 444 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7006 (pmm) cc_final: 0.6703 (pmm) REVERT: C 30 ASN cc_start: 0.7753 (t0) cc_final: 0.7546 (t0) REVERT: C 80 ASP cc_start: 0.5560 (t0) cc_final: 0.5275 (t0) REVERT: C 137 LEU cc_start: 0.7661 (tp) cc_final: 0.7367 (tp) REVERT: D 3 HIS cc_start: 0.7313 (m-70) cc_final: 0.6798 (m-70) REVERT: D 20 ASP cc_start: 0.7442 (m-30) cc_final: 0.7027 (m-30) REVERT: D 55 ILE cc_start: 0.9003 (tp) cc_final: 0.8587 (mt) REVERT: D 72 LEU cc_start: 0.7991 (tp) cc_final: 0.7695 (tp) REVERT: D 159 LEU cc_start: 0.5461 (mt) cc_final: 0.4691 (pp) REVERT: H 10 ARG cc_start: 0.8436 (mpp80) cc_final: 0.8070 (mtp180) REVERT: H 70 TRP cc_start: 0.8630 (p-90) cc_final: 0.7993 (p-90) REVERT: H 120 MET cc_start: 0.7833 (ptp) cc_final: 0.6901 (ptp) REVERT: H 279 LEU cc_start: 0.7926 (pp) cc_final: 0.7394 (tt) REVERT: H 311 ILE cc_start: 0.8586 (mm) cc_final: 0.8382 (mm) REVERT: H 339 ILE cc_start: 0.7643 (pt) cc_final: 0.7381 (pt) REVERT: A 80 ASP cc_start: 0.6893 (t0) cc_final: 0.6599 (t0) REVERT: A 107 LEU cc_start: 0.8603 (tp) cc_final: 0.8350 (tp) REVERT: A 147 ASN cc_start: 0.8814 (m-40) cc_final: 0.8566 (m-40) REVERT: A 151 ARG cc_start: 0.8208 (ttt-90) cc_final: 0.7785 (ttt-90) REVERT: B 113 LYS cc_start: 0.7657 (mmmt) cc_final: 0.7395 (mmmt) REVERT: G 47 VAL cc_start: 0.8549 (m) cc_final: 0.8265 (p) REVERT: G 120 MET cc_start: 0.8334 (ptp) cc_final: 0.8117 (ptp) REVERT: G 191 ILE cc_start: 0.8364 (pt) cc_final: 0.8105 (pt) REVERT: G 213 ILE cc_start: 0.9063 (tt) cc_final: 0.8623 (tt) REVERT: G 264 SER cc_start: 0.8307 (p) cc_final: 0.7949 (t) REVERT: G 370 ASP cc_start: 0.7347 (t70) cc_final: 0.6837 (t0) REVERT: E 16 SER cc_start: 0.8519 (t) cc_final: 0.8297 (t) REVERT: E 58 GLU cc_start: 0.7646 (tt0) cc_final: 0.7417 (tt0) REVERT: E 70 MET cc_start: 0.8059 (tpp) cc_final: 0.7814 (tpp) REVERT: E 127 ILE cc_start: 0.8485 (mt) cc_final: 0.7934 (mt) REVERT: F 11 MET cc_start: 0.8735 (tpp) cc_final: 0.8384 (tpp) REVERT: F 23 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8272 (mm-40) REVERT: F 70 MET cc_start: 0.6747 (tpp) cc_final: 0.6099 (tpt) REVERT: F 85 ASP cc_start: 0.7418 (t0) cc_final: 0.7001 (t70) REVERT: F 132 SER cc_start: 0.7309 (t) cc_final: 0.5892 (t) REVERT: F 145 GLU cc_start: 0.8197 (pm20) cc_final: 0.7668 (pm20) REVERT: I 93 MET cc_start: 0.7147 (mtt) cc_final: 0.6842 (mtt) REVERT: I 120 MET cc_start: 0.5937 (ptt) cc_final: 0.5732 (ptt) REVERT: I 342 ASP cc_start: 0.7888 (m-30) cc_final: 0.7496 (t70) outliers start: 3 outliers final: 1 residues processed: 446 average time/residue: 0.2851 time to fit residues: 198.5224 Evaluate side-chains 314 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 313 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 chunk 223 optimal weight: 40.0000 chunk 110 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN H 87 GLN H 206 ASN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN B 67 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN G 206 ASN ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 HIS E 68 GLN F 67 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 GLN I 291 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.7721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 18609 Z= 0.373 Angle : 0.723 11.430 25302 Z= 0.382 Chirality : 0.050 0.400 2934 Planarity : 0.005 0.056 3282 Dihedral : 4.976 21.653 2529 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.41 % Rotamer: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.25 (0.17), residues: 2331 helix: 0.04 (0.26), residues: 330 sheet: -0.58 (0.17), residues: 861 loop : -1.21 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 69 HIS 0.061 0.003 HIS C 3 PHE 0.015 0.002 PHE G 231 TYR 0.027 0.003 TYR C 109 ARG 0.016 0.001 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6948 (pmm) cc_final: 0.6444 (pmm) REVERT: C 11 MET cc_start: 0.7017 (ttm) cc_final: 0.6816 (ttt) REVERT: C 30 ASN cc_start: 0.8023 (t0) cc_final: 0.7646 (t0) REVERT: C 92 LYS cc_start: 0.8018 (mmtp) cc_final: 0.7495 (mttt) REVERT: D 3 HIS cc_start: 0.7562 (m-70) cc_final: 0.7347 (m-70) REVERT: D 27 TYR cc_start: 0.6631 (m-10) cc_final: 0.6377 (m-10) REVERT: D 159 LEU cc_start: 0.5726 (mt) cc_final: 0.5262 (pp) REVERT: H 31 GLN cc_start: 0.8928 (mm110) cc_final: 0.8441 (mm-40) REVERT: H 120 MET cc_start: 0.8398 (ptp) cc_final: 0.7439 (ptp) REVERT: H 131 LEU cc_start: 0.8547 (pp) cc_final: 0.8323 (pp) REVERT: H 146 TYR cc_start: 0.8426 (p90) cc_final: 0.7959 (p90) REVERT: H 177 ILE cc_start: 0.8594 (mt) cc_final: 0.8206 (mp) REVERT: B 1 MET cc_start: 0.4011 (mmm) cc_final: 0.3505 (tpp) REVERT: B 18 GLN cc_start: 0.8434 (mp10) cc_final: 0.7927 (mp10) REVERT: B 23 GLN cc_start: 0.6895 (pp30) cc_final: 0.6477 (pp30) REVERT: B 27 TYR cc_start: 0.6579 (m-10) cc_final: 0.6332 (m-10) REVERT: B 126 MET cc_start: 0.8160 (mmm) cc_final: 0.7851 (mmm) REVERT: B 132 SER cc_start: 0.8678 (t) cc_final: 0.7682 (t) REVERT: B 145 GLU cc_start: 0.7610 (pt0) cc_final: 0.7042 (pp20) REVERT: G 120 MET cc_start: 0.8547 (ptp) cc_final: 0.8180 (ptp) REVERT: G 191 ILE cc_start: 0.8594 (pt) cc_final: 0.8278 (pt) REVERT: G 264 SER cc_start: 0.9200 (p) cc_final: 0.8691 (t) REVERT: G 370 ASP cc_start: 0.7610 (t70) cc_final: 0.7235 (t0) REVERT: E 18 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8690 (tp-100) REVERT: E 96 ASP cc_start: 0.8597 (m-30) cc_final: 0.8203 (m-30) REVERT: E 126 MET cc_start: 0.8644 (ttm) cc_final: 0.8422 (ttm) REVERT: F 23 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8182 (mm-40) REVERT: F 70 MET cc_start: 0.6938 (tpp) cc_final: 0.6389 (tpt) REVERT: F 85 ASP cc_start: 0.7452 (t0) cc_final: 0.7098 (t70) REVERT: F 113 LYS cc_start: 0.7845 (mmpt) cc_final: 0.7620 (mmmt) REVERT: F 132 SER cc_start: 0.8364 (t) cc_final: 0.7108 (t) REVERT: F 145 GLU cc_start: 0.8283 (pm20) cc_final: 0.7832 (pm20) REVERT: I 24 ASN cc_start: 0.7953 (p0) cc_final: 0.7668 (p0) REVERT: I 120 MET cc_start: 0.7743 (ptt) cc_final: 0.7494 (ptt) REVERT: I 197 MET cc_start: 0.8404 (tpp) cc_final: 0.7905 (tpp) REVERT: I 245 MET cc_start: 0.3187 (ttt) cc_final: 0.2937 (ttt) REVERT: I 294 GLU cc_start: 0.5820 (pm20) cc_final: 0.5309 (pm20) REVERT: I 370 ASP cc_start: 0.7145 (t70) cc_final: 0.6930 (t0) outliers start: 1 outliers final: 1 residues processed: 374 average time/residue: 0.2916 time to fit residues: 168.7496 Evaluate side-chains 255 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 5.9990 chunk 126 optimal weight: 0.4980 chunk 3 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 92 optimal weight: 0.6980 chunk 190 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 0 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN D 89 GLN H 151 GLN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN B 67 GLN B 89 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 ASN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.8028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18609 Z= 0.213 Angle : 0.596 9.852 25302 Z= 0.313 Chirality : 0.046 0.184 2934 Planarity : 0.004 0.046 3282 Dihedral : 4.578 18.913 2529 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.03 (0.17), residues: 2331 helix: 0.39 (0.26), residues: 330 sheet: -0.41 (0.17), residues: 849 loop : -1.16 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 69 HIS 0.009 0.001 HIS C 3 PHE 0.017 0.002 PHE I 72 TYR 0.022 0.002 TYR F 40 ARG 0.005 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 2.133 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: C 1 MET cc_start: 0.7226 (pmm) cc_final: 0.6831 (pmm) REVERT: C 30 ASN cc_start: 0.8077 (t0) cc_final: 0.7725 (t0) REVERT: C 92 LYS cc_start: 0.7948 (mmtp) cc_final: 0.7551 (mtpt) REVERT: D 55 ILE cc_start: 0.9210 (tp) cc_final: 0.8903 (mt) REVERT: D 111 VAL cc_start: 0.8118 (t) cc_final: 0.7685 (p) REVERT: D 159 LEU cc_start: 0.5327 (mt) cc_final: 0.4918 (pp) REVERT: H 31 GLN cc_start: 0.8983 (mm110) cc_final: 0.8414 (mm-40) REVERT: H 120 MET cc_start: 0.8518 (ptp) cc_final: 0.7421 (ptp) REVERT: H 146 TYR cc_start: 0.8445 (p90) cc_final: 0.8053 (p90) REVERT: H 177 ILE cc_start: 0.8513 (mt) cc_final: 0.8250 (mp) REVERT: H 199 ILE cc_start: 0.9123 (pt) cc_final: 0.8890 (mt) REVERT: A 80 ASP cc_start: 0.7353 (t0) cc_final: 0.7110 (t0) REVERT: B 18 GLN cc_start: 0.8408 (mp10) cc_final: 0.7769 (mp10) REVERT: B 126 MET cc_start: 0.8255 (mmm) cc_final: 0.7743 (mmm) REVERT: B 132 SER cc_start: 0.8699 (t) cc_final: 0.7981 (t) REVERT: B 145 GLU cc_start: 0.7552 (pt0) cc_final: 0.7094 (pp20) REVERT: B 151 ARG cc_start: 0.8230 (ttt180) cc_final: 0.7937 (ttt90) REVERT: G 1 MET cc_start: 0.3177 (ptt) cc_final: 0.2651 (ptt) REVERT: G 47 VAL cc_start: 0.8886 (m) cc_final: 0.8541 (p) REVERT: G 130 GLU cc_start: 0.8386 (pt0) cc_final: 0.8130 (pt0) REVERT: G 191 ILE cc_start: 0.8566 (pt) cc_final: 0.8271 (pt) REVERT: G 216 MET cc_start: 0.8612 (mmm) cc_final: 0.8187 (mmm) REVERT: G 264 SER cc_start: 0.9130 (p) cc_final: 0.8623 (t) REVERT: G 370 ASP cc_start: 0.7449 (t70) cc_final: 0.7036 (t0) REVERT: G 398 MET cc_start: 0.4787 (ppp) cc_final: 0.4142 (ppp) REVERT: E 18 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8565 (tp-100) REVERT: F 23 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8286 (mm-40) REVERT: F 70 MET cc_start: 0.6830 (tpp) cc_final: 0.6328 (tpt) REVERT: F 85 ASP cc_start: 0.7779 (t0) cc_final: 0.7270 (t0) REVERT: F 132 SER cc_start: 0.8404 (t) cc_final: 0.7085 (t) REVERT: F 145 GLU cc_start: 0.8165 (pm20) cc_final: 0.7726 (pm20) REVERT: I 177 ILE cc_start: 0.8102 (mp) cc_final: 0.7807 (mp) REVERT: I 197 MET cc_start: 0.8617 (tpp) cc_final: 0.8099 (tpp) REVERT: I 237 ILE cc_start: 0.8798 (mm) cc_final: 0.8264 (mt) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.3090 time to fit residues: 164.3010 Evaluate side-chains 259 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 30.0000 chunk 201 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 223 optimal weight: 0.0970 chunk 185 optimal weight: 0.0770 chunk 103 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 117 optimal weight: 0.5980 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN D 89 GLN H 113 HIS H 122 ASN H 151 GLN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN B 67 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.8249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18609 Z= 0.182 Angle : 0.568 8.915 25302 Z= 0.299 Chirality : 0.045 0.171 2934 Planarity : 0.004 0.045 3282 Dihedral : 4.342 17.865 2529 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.73 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2331 helix: 0.46 (0.27), residues: 324 sheet: -0.64 (0.17), residues: 891 loop : -1.01 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 69 HIS 0.005 0.001 HIS D 3 PHE 0.017 0.001 PHE G 231 TYR 0.031 0.002 TYR H 92 ARG 0.005 0.000 ARG D 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7249 (pmm) cc_final: 0.6849 (pmm) REVERT: C 30 ASN cc_start: 0.8240 (t0) cc_final: 0.7843 (t0) REVERT: C 92 LYS cc_start: 0.8077 (mmtp) cc_final: 0.7590 (mtpt) REVERT: C 103 THR cc_start: 0.8018 (m) cc_final: 0.7816 (m) REVERT: D 3 HIS cc_start: 0.7820 (m90) cc_final: 0.7373 (m-70) REVERT: D 46 ARG cc_start: 0.7816 (mmp-170) cc_final: 0.7608 (mmp-170) REVERT: D 70 MET cc_start: 0.6276 (mmm) cc_final: 0.5805 (mmt) REVERT: D 111 VAL cc_start: 0.8012 (t) cc_final: 0.7654 (p) REVERT: D 159 LEU cc_start: 0.5201 (mt) cc_final: 0.4848 (pp) REVERT: H 31 GLN cc_start: 0.8949 (mm110) cc_final: 0.8268 (mm-40) REVERT: H 120 MET cc_start: 0.8405 (ptp) cc_final: 0.7485 (ptp) REVERT: H 146 TYR cc_start: 0.8379 (p90) cc_final: 0.8040 (p90) REVERT: H 177 ILE cc_start: 0.8582 (mt) cc_final: 0.8241 (mp) REVERT: H 280 TYR cc_start: 0.8356 (t80) cc_final: 0.8002 (t80) REVERT: A 18 GLN cc_start: 0.7687 (tp40) cc_final: 0.7395 (tp40) REVERT: A 80 ASP cc_start: 0.7049 (t0) cc_final: 0.6834 (t0) REVERT: B 1 MET cc_start: 0.3815 (tpp) cc_final: 0.3585 (tpp) REVERT: B 18 GLN cc_start: 0.8390 (mp10) cc_final: 0.7689 (mp10) REVERT: B 23 GLN cc_start: 0.7036 (pp30) cc_final: 0.6807 (mt0) REVERT: B 26 GLU cc_start: 0.8172 (tt0) cc_final: 0.7760 (tt0) REVERT: B 27 TYR cc_start: 0.6521 (m-10) cc_final: 0.6230 (m-10) REVERT: B 92 LYS cc_start: 0.8129 (mttp) cc_final: 0.7806 (mmtt) REVERT: B 126 MET cc_start: 0.8238 (mmm) cc_final: 0.7803 (mmm) REVERT: G 1 MET cc_start: 0.3181 (ptt) cc_final: 0.2680 (ptt) REVERT: G 47 VAL cc_start: 0.8925 (m) cc_final: 0.8586 (p) REVERT: G 130 GLU cc_start: 0.8433 (pt0) cc_final: 0.8133 (pt0) REVERT: G 216 MET cc_start: 0.8609 (mmm) cc_final: 0.8201 (mmm) REVERT: G 264 SER cc_start: 0.9003 (p) cc_final: 0.8506 (t) REVERT: F 23 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8208 (mm-40) REVERT: F 35 VAL cc_start: 0.7820 (t) cc_final: 0.7518 (m) REVERT: F 70 MET cc_start: 0.6552 (tpp) cc_final: 0.5899 (mmt) REVERT: F 85 ASP cc_start: 0.7569 (t0) cc_final: 0.7111 (t0) REVERT: F 132 SER cc_start: 0.8496 (t) cc_final: 0.7144 (t) REVERT: F 145 GLU cc_start: 0.8187 (pm20) cc_final: 0.7640 (pm20) REVERT: I 13 VAL cc_start: 0.9153 (t) cc_final: 0.8901 (t) REVERT: I 197 MET cc_start: 0.8656 (tpp) cc_final: 0.8236 (tpp) REVERT: I 237 ILE cc_start: 0.8835 (mm) cc_final: 0.8306 (mt) REVERT: I 294 GLU cc_start: 0.5806 (pm20) cc_final: 0.5569 (pm20) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2919 time to fit residues: 157.3745 Evaluate side-chains 256 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 222 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN D 87 GLN D 89 GLN H 20 HIS H 122 ASN H 151 GLN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN A 153 GLN ** B 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN E 54 HIS ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.8788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 18609 Z= 0.276 Angle : 0.604 10.017 25302 Z= 0.317 Chirality : 0.046 0.186 2934 Planarity : 0.004 0.045 3282 Dihedral : 4.464 19.449 2529 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.25 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.17 (0.17), residues: 2331 helix: 0.17 (0.26), residues: 348 sheet: -0.61 (0.17), residues: 831 loop : -1.12 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 144 HIS 0.005 0.001 HIS F 3 PHE 0.016 0.002 PHE H 255 TYR 0.029 0.002 TYR H 146 ARG 0.011 0.001 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7169 (pmm) cc_final: 0.6823 (pmm) REVERT: C 30 ASN cc_start: 0.8284 (t0) cc_final: 0.7803 (t0) REVERT: C 92 LYS cc_start: 0.8111 (mmtp) cc_final: 0.7641 (mtpt) REVERT: D 3 HIS cc_start: 0.7947 (m90) cc_final: 0.7280 (m-70) REVERT: D 70 MET cc_start: 0.6286 (mmm) cc_final: 0.5775 (mmt) REVERT: D 92 LYS cc_start: 0.8431 (mttp) cc_final: 0.7948 (mmtm) REVERT: D 125 ASP cc_start: 0.8141 (t0) cc_final: 0.7930 (t0) REVERT: H 120 MET cc_start: 0.8547 (ptp) cc_final: 0.7792 (ptp) REVERT: H 177 ILE cc_start: 0.8563 (mt) cc_final: 0.8314 (mp) REVERT: B 1 MET cc_start: 0.4201 (tpp) cc_final: 0.3986 (tpp) REVERT: B 18 GLN cc_start: 0.8513 (mp10) cc_final: 0.7900 (mp10) REVERT: B 27 TYR cc_start: 0.7193 (m-10) cc_final: 0.6893 (m-10) REVERT: B 126 MET cc_start: 0.8352 (mmm) cc_final: 0.8046 (mmm) REVERT: G 1 MET cc_start: 0.3670 (ptt) cc_final: 0.3184 (ptt) REVERT: G 93 MET cc_start: 0.8268 (mpp) cc_final: 0.8015 (mpp) REVERT: G 130 GLU cc_start: 0.8421 (pt0) cc_final: 0.8164 (pt0) REVERT: G 191 ILE cc_start: 0.8576 (pt) cc_final: 0.8292 (pt) REVERT: G 197 MET cc_start: 0.8995 (tpp) cc_final: 0.8418 (tpp) REVERT: G 216 MET cc_start: 0.8684 (mmm) cc_final: 0.8334 (mmm) REVERT: G 264 SER cc_start: 0.9049 (p) cc_final: 0.8741 (t) REVERT: G 370 ASP cc_start: 0.7572 (t70) cc_final: 0.7238 (t0) REVERT: F 20 ASP cc_start: 0.7972 (m-30) cc_final: 0.7712 (m-30) REVERT: F 46 ARG cc_start: 0.7533 (mmp-170) cc_final: 0.7011 (mmp-170) REVERT: F 70 MET cc_start: 0.7286 (tpp) cc_final: 0.7028 (tpt) REVERT: F 85 ASP cc_start: 0.7874 (t0) cc_final: 0.7250 (t0) REVERT: F 132 SER cc_start: 0.8602 (t) cc_final: 0.7157 (t) REVERT: F 145 GLU cc_start: 0.8167 (pm20) cc_final: 0.7693 (pm20) REVERT: I 120 MET cc_start: 0.7556 (ptt) cc_final: 0.6718 (ptt) REVERT: I 237 ILE cc_start: 0.8908 (mm) cc_final: 0.8410 (mt) REVERT: I 294 GLU cc_start: 0.6451 (pm20) cc_final: 0.6238 (pm20) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2949 time to fit residues: 146.7926 Evaluate side-chains 237 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 132 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 151 optimal weight: 0.0170 chunk 110 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 overall best weight: 1.0420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN H 31 GLN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN B 67 GLN ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 ASN E 68 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.8942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18609 Z= 0.179 Angle : 0.568 8.365 25302 Z= 0.298 Chirality : 0.045 0.180 2934 Planarity : 0.004 0.051 3282 Dihedral : 4.304 17.702 2529 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.09 (0.17), residues: 2331 helix: 0.46 (0.27), residues: 327 sheet: -0.61 (0.17), residues: 891 loop : -1.09 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 69 HIS 0.006 0.001 HIS H 129 PHE 0.018 0.001 PHE C 42 TYR 0.028 0.002 TYR H 128 ARG 0.009 0.001 ARG I 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7151 (pmm) cc_final: 0.6816 (pmm) REVERT: C 30 ASN cc_start: 0.8379 (t0) cc_final: 0.7918 (t0) REVERT: C 92 LYS cc_start: 0.8049 (mmtp) cc_final: 0.7598 (mtpt) REVERT: D 1 MET cc_start: 0.4409 (tmm) cc_final: 0.3823 (tmm) REVERT: D 3 HIS cc_start: 0.7857 (m90) cc_final: 0.7335 (m-70) REVERT: D 46 ARG cc_start: 0.7911 (mmp-170) cc_final: 0.7646 (mmp-170) REVERT: D 70 MET cc_start: 0.6226 (mmm) cc_final: 0.5730 (mmt) REVERT: D 92 LYS cc_start: 0.8374 (mttp) cc_final: 0.7813 (mmtp) REVERT: H 120 MET cc_start: 0.8344 (ptp) cc_final: 0.7506 (ptp) REVERT: H 131 LEU cc_start: 0.8512 (mt) cc_final: 0.7564 (mp) REVERT: H 133 MET cc_start: 0.8478 (tpp) cc_final: 0.8163 (tmm) REVERT: H 177 ILE cc_start: 0.8532 (mt) cc_final: 0.8189 (mp) REVERT: H 280 TYR cc_start: 0.8421 (t80) cc_final: 0.8021 (t80) REVERT: A 18 GLN cc_start: 0.7753 (tp40) cc_final: 0.7439 (tp40) REVERT: A 29 ASN cc_start: 0.8661 (m110) cc_final: 0.8065 (m110) REVERT: B 1 MET cc_start: 0.3974 (tpp) cc_final: 0.3700 (tpp) REVERT: B 16 SER cc_start: 0.8902 (t) cc_final: 0.8424 (p) REVERT: B 18 GLN cc_start: 0.8550 (mp10) cc_final: 0.7886 (mp10) REVERT: B 26 GLU cc_start: 0.8230 (tt0) cc_final: 0.7866 (tt0) REVERT: B 27 TYR cc_start: 0.7049 (m-10) cc_final: 0.6736 (m-10) REVERT: B 92 LYS cc_start: 0.8263 (mttp) cc_final: 0.8021 (mmtt) REVERT: B 126 MET cc_start: 0.8303 (mmm) cc_final: 0.7918 (mmm) REVERT: G 1 MET cc_start: 0.3662 (ptt) cc_final: 0.3150 (ptt) REVERT: G 47 VAL cc_start: 0.8996 (m) cc_final: 0.8650 (p) REVERT: G 93 MET cc_start: 0.8253 (mpp) cc_final: 0.8022 (mpp) REVERT: G 130 GLU cc_start: 0.8443 (pt0) cc_final: 0.8118 (pt0) REVERT: G 191 ILE cc_start: 0.8548 (pt) cc_final: 0.8247 (pt) REVERT: G 216 MET cc_start: 0.8607 (mmm) cc_final: 0.8295 (mmm) REVERT: G 264 SER cc_start: 0.9119 (p) cc_final: 0.8617 (t) REVERT: G 398 MET cc_start: 0.4677 (ppp) cc_final: 0.3538 (tmm) REVERT: E 70 MET cc_start: 0.8282 (mmt) cc_final: 0.7927 (mmm) REVERT: F 20 ASP cc_start: 0.8056 (m-30) cc_final: 0.7740 (m-30) REVERT: F 27 TYR cc_start: 0.8053 (m-10) cc_final: 0.7599 (m-10) REVERT: F 85 ASP cc_start: 0.7291 (t0) cc_final: 0.7039 (t70) REVERT: F 132 SER cc_start: 0.8535 (t) cc_final: 0.6979 (t) REVERT: F 145 GLU cc_start: 0.8145 (pm20) cc_final: 0.7641 (pm20) REVERT: I 120 MET cc_start: 0.7201 (ptt) cc_final: 0.6364 (ptt) REVERT: I 237 ILE cc_start: 0.8887 (mm) cc_final: 0.8450 (mt) REVERT: I 280 TYR cc_start: 0.8680 (t80) cc_final: 0.8055 (t80) REVERT: I 294 GLU cc_start: 0.6475 (pm20) cc_final: 0.6198 (pm20) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.2805 time to fit residues: 145.8797 Evaluate side-chains 253 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 187 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN H 31 GLN H 151 GLN ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN B 67 GLN B 89 GLN B 106 ASN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.9306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18609 Z= 0.260 Angle : 0.598 9.673 25302 Z= 0.312 Chirality : 0.046 0.171 2934 Planarity : 0.004 0.047 3282 Dihedral : 4.426 18.161 2529 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.10 (0.17), residues: 2331 helix: 0.44 (0.27), residues: 324 sheet: -0.62 (0.17), residues: 837 loop : -1.09 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 69 HIS 0.005 0.001 HIS B 3 PHE 0.014 0.002 PHE C 42 TYR 0.021 0.002 TYR C 27 ARG 0.005 0.001 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7242 (pmm) cc_final: 0.6921 (pmm) REVERT: C 30 ASN cc_start: 0.8727 (t0) cc_final: 0.8414 (t0) REVERT: D 70 MET cc_start: 0.6317 (mmm) cc_final: 0.5823 (mmt) REVERT: D 92 LYS cc_start: 0.8338 (mttp) cc_final: 0.7892 (mmtp) REVERT: D 125 ASP cc_start: 0.8078 (t0) cc_final: 0.7828 (t0) REVERT: H 93 MET cc_start: 0.7638 (mtm) cc_final: 0.7365 (mtm) REVERT: H 120 MET cc_start: 0.8532 (ptp) cc_final: 0.7794 (ptp) REVERT: H 130 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7647 (tm-30) REVERT: H 133 MET cc_start: 0.8493 (tpp) cc_final: 0.8219 (tmm) REVERT: H 280 TYR cc_start: 0.8609 (t80) cc_final: 0.8006 (t80) REVERT: H 327 ASP cc_start: 0.7900 (t0) cc_final: 0.7355 (p0) REVERT: A 18 GLN cc_start: 0.7901 (tp40) cc_final: 0.7242 (tp40) REVERT: A 29 ASN cc_start: 0.8604 (m110) cc_final: 0.8087 (m110) REVERT: B 1 MET cc_start: 0.4329 (tpp) cc_final: 0.3838 (tpp) REVERT: B 16 SER cc_start: 0.8842 (t) cc_final: 0.8395 (p) REVERT: B 18 GLN cc_start: 0.8623 (mp10) cc_final: 0.7904 (mp10) REVERT: B 27 TYR cc_start: 0.7224 (m-10) cc_final: 0.6945 (m-10) REVERT: B 92 LYS cc_start: 0.8428 (mttp) cc_final: 0.8065 (mmtt) REVERT: B 126 MET cc_start: 0.8160 (mmm) cc_final: 0.7912 (mmm) REVERT: G 1 MET cc_start: 0.3249 (ptt) cc_final: 0.2790 (ptt) REVERT: G 130 GLU cc_start: 0.8433 (pt0) cc_final: 0.8172 (pt0) REVERT: G 191 ILE cc_start: 0.8608 (pt) cc_final: 0.8319 (pt) REVERT: G 216 MET cc_start: 0.8719 (mmm) cc_final: 0.8377 (mmm) REVERT: G 264 SER cc_start: 0.8979 (p) cc_final: 0.8739 (t) REVERT: G 370 ASP cc_start: 0.7543 (t70) cc_final: 0.7155 (t0) REVERT: E 70 MET cc_start: 0.8543 (mmt) cc_final: 0.8214 (mmm) REVERT: E 73 GLU cc_start: 0.7744 (tt0) cc_final: 0.7260 (mt-10) REVERT: F 20 ASP cc_start: 0.8010 (m-30) cc_final: 0.7761 (m-30) REVERT: F 27 TYR cc_start: 0.8282 (m-10) cc_final: 0.7789 (m-10) REVERT: F 46 ARG cc_start: 0.7532 (mmp-170) cc_final: 0.6994 (mmp-170) REVERT: F 70 MET cc_start: 0.6017 (tpt) cc_final: 0.5431 (mmt) REVERT: F 85 ASP cc_start: 0.7458 (t0) cc_final: 0.7247 (t70) REVERT: F 132 SER cc_start: 0.8647 (t) cc_final: 0.7106 (t) REVERT: F 145 GLU cc_start: 0.8195 (pm20) cc_final: 0.7732 (pm20) REVERT: I 120 MET cc_start: 0.7531 (ptt) cc_final: 0.6760 (ptt) REVERT: I 197 MET cc_start: 0.8755 (tpp) cc_final: 0.8233 (tpp) REVERT: I 237 ILE cc_start: 0.8985 (mm) cc_final: 0.8612 (mt) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2855 time to fit residues: 137.9828 Evaluate side-chains 233 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 211 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 19 optimal weight: 0.0770 chunk 141 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 overall best weight: 3.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** H 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN B 67 GLN B 106 ASN G 26 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 ASN ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.9799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18609 Z= 0.308 Angle : 0.632 9.258 25302 Z= 0.334 Chirality : 0.046 0.182 2934 Planarity : 0.005 0.098 3282 Dihedral : 4.609 18.960 2529 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.30 (0.17), residues: 2331 helix: 0.16 (0.26), residues: 339 sheet: -0.79 (0.17), residues: 873 loop : -1.16 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 69 HIS 0.009 0.001 HIS D 3 PHE 0.018 0.002 PHE I 293 TYR 0.023 0.002 TYR I 146 ARG 0.010 0.001 ARG D 157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7341 (pmm) cc_final: 0.7047 (pmm) REVERT: C 30 ASN cc_start: 0.8894 (t0) cc_final: 0.8370 (t0) REVERT: D 3 HIS cc_start: 0.7632 (m-70) cc_final: 0.6996 (m90) REVERT: D 46 ARG cc_start: 0.7708 (mmp-170) cc_final: 0.7478 (mmp-170) REVERT: D 92 LYS cc_start: 0.8568 (mttp) cc_final: 0.8098 (mmtm) REVERT: D 125 ASP cc_start: 0.8104 (t0) cc_final: 0.7765 (t0) REVERT: H 120 MET cc_start: 0.8672 (ptp) cc_final: 0.8109 (ptp) REVERT: H 327 ASP cc_start: 0.8034 (t0) cc_final: 0.7438 (p0) REVERT: H 370 ASP cc_start: 0.6306 (t70) cc_final: 0.6046 (t0) REVERT: A 29 ASN cc_start: 0.8612 (m110) cc_final: 0.8095 (m110) REVERT: B 1 MET cc_start: 0.4574 (tpp) cc_final: 0.4189 (tpp) REVERT: B 16 SER cc_start: 0.8748 (t) cc_final: 0.8308 (p) REVERT: B 23 GLN cc_start: 0.7012 (pp30) cc_final: 0.6232 (pp30) REVERT: B 27 TYR cc_start: 0.7417 (m-10) cc_final: 0.6962 (m-10) REVERT: G 1 MET cc_start: 0.3455 (ptt) cc_final: 0.3055 (ptt) REVERT: G 191 ILE cc_start: 0.8675 (pt) cc_final: 0.8386 (pt) REVERT: G 216 MET cc_start: 0.8742 (mmm) cc_final: 0.8485 (mmm) REVERT: G 445 THR cc_start: 0.8214 (m) cc_final: 0.7922 (p) REVERT: E 70 MET cc_start: 0.8464 (mmt) cc_final: 0.8110 (mmm) REVERT: E 73 GLU cc_start: 0.7783 (tt0) cc_final: 0.7216 (mt-10) REVERT: F 20 ASP cc_start: 0.8176 (m-30) cc_final: 0.7866 (m-30) REVERT: F 27 TYR cc_start: 0.8539 (m-10) cc_final: 0.7981 (m-10) REVERT: F 46 ARG cc_start: 0.7530 (mmp-170) cc_final: 0.6989 (mmp-170) REVERT: F 85 ASP cc_start: 0.7751 (t0) cc_final: 0.7240 (t70) REVERT: F 145 GLU cc_start: 0.8211 (pm20) cc_final: 0.7806 (pm20) REVERT: I 120 MET cc_start: 0.7489 (ptt) cc_final: 0.6755 (ptt) REVERT: I 197 MET cc_start: 0.8765 (tpp) cc_final: 0.8409 (tpp) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2738 time to fit residues: 127.6929 Evaluate side-chains 227 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 chunk 27 optimal weight: 0.0970 chunk 50 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 188 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN B 67 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN ** G 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.094518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.073653 restraints weight = 48352.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.075445 restraints weight = 28285.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.076655 restraints weight = 19305.570| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.9956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18609 Z= 0.228 Angle : 0.598 9.152 25302 Z= 0.314 Chirality : 0.045 0.173 2934 Planarity : 0.004 0.045 3282 Dihedral : 4.515 18.236 2529 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.28 (0.17), residues: 2331 helix: 0.15 (0.27), residues: 342 sheet: -0.81 (0.17), residues: 858 loop : -1.10 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 69 HIS 0.008 0.001 HIS D 3 PHE 0.018 0.002 PHE E 42 TYR 0.020 0.002 TYR I 357 ARG 0.005 0.001 ARG A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3881.94 seconds wall clock time: 72 minutes 15.55 seconds (4335.55 seconds total)