Starting phenix.real_space_refine on Wed Feb 14 07:58:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k2x_36842/02_2024/8k2x_36842_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k2x_36842/02_2024/8k2x_36842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k2x_36842/02_2024/8k2x_36842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k2x_36842/02_2024/8k2x_36842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k2x_36842/02_2024/8k2x_36842_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k2x_36842/02_2024/8k2x_36842_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 63 5.16 5 C 5665 2.51 5 N 1534 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "S GLU 42": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "S GLU 246": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8900 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "R" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2266 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 64 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.89, per 1000 atoms: 0.55 Number of scatterers: 8900 At special positions: 0 Unit cell: (90.95, 121.55, 129.2, 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 63 16.00 O 1638 8.00 N 1534 7.00 C 5665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 124 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.28 Conformation dependent library (CDL) restraints added in 1.7 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 12 sheets defined 34.8% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 removed outlier: 3.717A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 removed outlier: 3.723A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.383A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'B' and resid 8 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.687A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'G' and resid 10 through 22 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 48 through 80 Proline residue: R 57 - end of helix removed outlier: 3.642A pdb=" N ALA R 75 " --> pdb=" O ASN R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 110 Proline residue: R 107 - end of helix Processing helix chain 'R' and resid 121 through 153 Processing helix chain 'R' and resid 156 through 162 Processing helix chain 'R' and resid 167 through 189 Proline residue: R 185 - end of helix Processing helix chain 'R' and resid 209 through 244 Proline residue: R 227 - end of helix Processing helix chain 'R' and resid 250 through 284 Proline residue: R 270 - end of helix removed outlier: 4.568A pdb=" N LEU R 283 " --> pdb=" O ILE R 279 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 318 removed outlier: 3.884A pdb=" N SER R 294 " --> pdb=" O CYS R 290 " (cutoff:3.500A) Proline residue: R 315 - end of helix Processing helix chain 'R' and resid 323 through 335 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.626A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.944A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.893A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.833A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.025A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.792A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.671A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.768A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.792A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.582A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 155 through 160 420 hydrogen bonds defined for protein. 1212 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: 2.63 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2425 1.33 - 1.46: 1904 1.46 - 1.58: 4662 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 9081 Sorted by residual: bond pdb=" N ASN R 199 " pdb=" CA ASN R 199 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.78e+00 bond pdb=" N LEU L 3 " pdb=" CA LEU L 3 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.60e+00 bond pdb=" N VAL S 149 " pdb=" CA VAL S 149 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.19e-02 7.06e+03 6.26e+00 bond pdb=" N VAL S 147 " pdb=" CA VAL S 147 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.23e-02 6.61e+03 5.49e+00 bond pdb=" N GLU B 172 " pdb=" CA GLU B 172 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.37e+00 ... (remaining 9076 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.76: 134 105.76 - 112.82: 4928 112.82 - 119.88: 2940 119.88 - 126.95: 4198 126.95 - 134.01: 104 Bond angle restraints: 12304 Sorted by residual: angle pdb=" C PRO S 148 " pdb=" N VAL S 149 " pdb=" CA VAL S 149 " ideal model delta sigma weight residual 122.71 117.97 4.74 1.44e+00 4.82e-01 1.08e+01 angle pdb=" C PRO S 148 " pdb=" CA PRO S 148 " pdb=" CB PRO S 148 " ideal model delta sigma weight residual 111.56 108.13 3.43 1.09e+00 8.42e-01 9.90e+00 angle pdb=" CA MET R 281 " pdb=" CB MET R 281 " pdb=" CG MET R 281 " ideal model delta sigma weight residual 114.10 120.11 -6.01 2.00e+00 2.50e-01 9.02e+00 angle pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " pdb=" CG TYR S 235 " ideal model delta sigma weight residual 113.90 108.54 5.36 1.80e+00 3.09e-01 8.86e+00 angle pdb=" C LYS A 192 " pdb=" N ASP A 193 " pdb=" CA ASP A 193 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.29e+00 ... (remaining 12299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 4623 17.55 - 35.10: 622 35.10 - 52.66: 170 52.66 - 70.21: 16 70.21 - 87.76: 11 Dihedral angle restraints: 5442 sinusoidal: 2153 harmonic: 3289 Sorted by residual: dihedral pdb=" CA GLU R 196 " pdb=" C GLU R 196 " pdb=" N ARG R 197 " pdb=" CA ARG R 197 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA SER S 208 " pdb=" C SER S 208 " pdb=" N GLY S 209 " pdb=" CA GLY S 209 " ideal model delta harmonic sigma weight residual 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" SG CYS R 124 " pdb=" CB CYS R 203 " pdb=" SG CYS R 203 " pdb=" CA CYS R 203 " ideal model delta sinusoidal sigma weight residual -73.00 -3.44 -69.56 1 2.00e+01 2.50e-03 1.56e+01 ... (remaining 5439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1020 0.039 - 0.078: 272 0.078 - 0.118: 96 0.118 - 0.157: 18 0.157 - 0.196: 3 Chirality restraints: 1409 Sorted by residual: chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" CA LEU R 198 " pdb=" N LEU R 198 " pdb=" C LEU R 198 " pdb=" CB LEU R 198 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA LEU R 180 " pdb=" N LEU R 180 " pdb=" C LEU R 180 " pdb=" CB LEU R 180 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.65e-01 ... (remaining 1406 not shown) Planarity restraints: 1551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 314 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO R 315 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO R 315 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 315 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO S 236 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 106 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.85e+00 pdb=" N PRO R 107 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 107 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 107 " -0.027 5.00e-02 4.00e+02 ... (remaining 1548 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2459 2.81 - 3.33: 8103 3.33 - 3.85: 14418 3.85 - 4.38: 16615 4.38 - 4.90: 30039 Nonbonded interactions: 71634 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.283 2.440 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.291 2.440 nonbonded pdb=" OD2 ASP R 195 " pdb=" NE2 GLN R 204 " model vdw 2.293 2.520 nonbonded pdb=" OE1 GLU A 33 " pdb=" ND1 HIS A 195 " model vdw 2.302 2.520 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.311 2.520 ... (remaining 71629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.900 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.290 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 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 : 0.003 0.036 9081 Z= 0.188 Angle : 0.573 9.384 12304 Z= 0.307 Chirality : 0.042 0.196 1409 Planarity : 0.004 0.054 1551 Dihedral : 16.755 87.760 3311 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 25.68 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1120 helix: 2.27 (0.26), residues: 380 sheet: 0.20 (0.30), residues: 283 loop : -0.94 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.004 0.001 HIS R 193 PHE 0.026 0.001 PHE R 182 TYR 0.027 0.001 TYR S 235 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.031 Fit side-chains REVERT: A 305 CYS cc_start: 0.7727 (p) cc_final: 0.7380 (m) REVERT: R 99 ASP cc_start: 0.7275 (t70) cc_final: 0.6941 (t70) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2446 time to fit residues: 43.8610 Evaluate side-chains 123 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN R 116 GLN S 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9081 Z= 0.298 Angle : 0.567 8.470 12304 Z= 0.289 Chirality : 0.042 0.271 1409 Planarity : 0.004 0.051 1551 Dihedral : 4.963 53.299 1300 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.26 % Allowed : 25.05 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1120 helix: 2.19 (0.27), residues: 382 sheet: 0.06 (0.30), residues: 288 loop : -1.01 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 109 HIS 0.006 0.001 HIS R 272 PHE 0.020 0.002 PHE R 182 TYR 0.041 0.002 TYR S 235 ARG 0.003 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 131 time to evaluate : 1.033 Fit side-chains outliers start: 41 outliers final: 22 residues processed: 158 average time/residue: 0.2421 time to fit residues: 51.6875 Evaluate side-chains 151 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9081 Z= 0.190 Angle : 0.522 9.017 12304 Z= 0.263 Chirality : 0.040 0.236 1409 Planarity : 0.003 0.050 1551 Dihedral : 4.494 49.814 1300 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.53 % Allowed : 26.61 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.26), residues: 1120 helix: 2.30 (0.27), residues: 382 sheet: 0.16 (0.30), residues: 287 loop : -0.97 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS R 272 PHE 0.014 0.001 PHE R 207 TYR 0.030 0.001 TYR S 235 ARG 0.003 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 134 time to evaluate : 1.032 Fit side-chains outliers start: 34 outliers final: 22 residues processed: 154 average time/residue: 0.2399 time to fit residues: 49.2607 Evaluate side-chains 148 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9081 Z= 0.369 Angle : 0.602 8.641 12304 Z= 0.306 Chirality : 0.043 0.300 1409 Planarity : 0.004 0.051 1551 Dihedral : 4.844 53.660 1300 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.37 % Allowed : 26.40 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1120 helix: 2.15 (0.27), residues: 384 sheet: 0.05 (0.30), residues: 293 loop : -1.02 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 117 HIS 0.005 0.001 HIS R 272 PHE 0.018 0.002 PHE B 253 TYR 0.043 0.002 TYR S 235 ARG 0.002 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 131 time to evaluate : 0.909 Fit side-chains REVERT: R 68 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8427 (mm) REVERT: S 235 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.8103 (t80) outliers start: 42 outliers final: 29 residues processed: 158 average time/residue: 0.2305 time to fit residues: 49.0294 Evaluate side-chains 154 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.5980 chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9081 Z= 0.171 Angle : 0.520 8.697 12304 Z= 0.261 Chirality : 0.040 0.217 1409 Planarity : 0.003 0.047 1551 Dihedral : 4.435 49.765 1300 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.74 % Allowed : 27.23 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.26), residues: 1120 helix: 2.31 (0.27), residues: 383 sheet: 0.19 (0.30), residues: 285 loop : -0.99 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS R 272 PHE 0.015 0.001 PHE R 64 TYR 0.028 0.001 TYR S 235 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 1.042 Fit side-chains REVERT: R 68 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8422 (mm) REVERT: R 99 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.6884 (t70) REVERT: S 218 ARG cc_start: 0.7926 (ptp-110) cc_final: 0.7667 (ptp90) REVERT: S 235 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7622 (t80) outliers start: 36 outliers final: 20 residues processed: 159 average time/residue: 0.2380 time to fit residues: 50.9918 Evaluate side-chains 153 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9081 Z= 0.179 Angle : 0.523 8.775 12304 Z= 0.263 Chirality : 0.040 0.223 1409 Planarity : 0.003 0.051 1551 Dihedral : 4.339 49.776 1300 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.05 % Allowed : 26.92 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 1120 helix: 2.36 (0.27), residues: 383 sheet: 0.26 (0.30), residues: 290 loop : -0.99 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.004 0.001 HIS R 272 PHE 0.018 0.001 PHE R 182 TYR 0.030 0.001 TYR S 235 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 133 time to evaluate : 1.029 Fit side-chains REVERT: R 68 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8428 (mm) REVERT: R 99 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6867 (t70) outliers start: 39 outliers final: 32 residues processed: 159 average time/residue: 0.2277 time to fit residues: 49.2040 Evaluate side-chains 165 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9081 Z= 0.281 Angle : 0.565 8.424 12304 Z= 0.285 Chirality : 0.042 0.222 1409 Planarity : 0.004 0.050 1551 Dihedral : 4.601 52.218 1300 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.78 % Allowed : 26.40 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 1120 helix: 2.27 (0.27), residues: 384 sheet: 0.10 (0.30), residues: 287 loop : -0.99 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.008 0.001 HIS R 272 PHE 0.016 0.001 PHE B 253 TYR 0.027 0.002 TYR S 235 ARG 0.002 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 132 time to evaluate : 0.919 Fit side-chains REVERT: A 306 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6672 (pt0) REVERT: R 68 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8400 (mm) REVERT: R 99 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6907 (t70) outliers start: 46 outliers final: 38 residues processed: 160 average time/residue: 0.2296 time to fit residues: 49.8540 Evaluate side-chains 168 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 127 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 193 HIS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9081 Z= 0.181 Angle : 0.526 8.716 12304 Z= 0.264 Chirality : 0.040 0.190 1409 Planarity : 0.003 0.048 1551 Dihedral : 4.386 49.102 1300 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.37 % Allowed : 26.92 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1120 helix: 2.33 (0.27), residues: 383 sheet: 0.18 (0.30), residues: 285 loop : -0.97 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS R 272 PHE 0.019 0.001 PHE R 182 TYR 0.022 0.001 TYR S 235 ARG 0.003 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 134 time to evaluate : 0.950 Fit side-chains REVERT: R 68 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8428 (mm) REVERT: R 99 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6901 (t70) outliers start: 42 outliers final: 36 residues processed: 159 average time/residue: 0.2176 time to fit residues: 47.0541 Evaluate side-chains 169 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9081 Z= 0.190 Angle : 0.537 8.868 12304 Z= 0.268 Chirality : 0.040 0.182 1409 Planarity : 0.003 0.053 1551 Dihedral : 4.345 49.420 1300 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.26 % Allowed : 27.23 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1120 helix: 2.35 (0.27), residues: 383 sheet: 0.22 (0.30), residues: 285 loop : -0.98 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS R 272 PHE 0.021 0.001 PHE R 182 TYR 0.025 0.001 TYR S 235 ARG 0.003 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 133 time to evaluate : 1.046 Fit side-chains REVERT: A 289 GLU cc_start: 0.7071 (pm20) cc_final: 0.5988 (pt0) REVERT: R 99 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.6903 (t70) outliers start: 41 outliers final: 36 residues processed: 159 average time/residue: 0.2175 time to fit residues: 47.5357 Evaluate side-chains 165 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 128 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 262 VAL Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 0.3980 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9081 Z= 0.165 Angle : 0.532 9.098 12304 Z= 0.266 Chirality : 0.040 0.156 1409 Planarity : 0.003 0.049 1551 Dihedral : 4.250 48.548 1300 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.53 % Allowed : 27.86 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1120 helix: 2.40 (0.27), residues: 380 sheet: 0.28 (0.31), residues: 274 loop : -0.98 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.009 0.001 HIS R 272 PHE 0.024 0.001 PHE R 182 TYR 0.020 0.001 TYR S 235 ARG 0.002 0.000 ARG A 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 0.970 Fit side-chains REVERT: A 289 GLU cc_start: 0.6983 (pm20) cc_final: 0.6015 (pt0) REVERT: R 99 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6857 (t70) REVERT: R 266 LEU cc_start: 0.8545 (tt) cc_final: 0.7628 (mt) outliers start: 34 outliers final: 30 residues processed: 152 average time/residue: 0.2175 time to fit residues: 44.9399 Evaluate side-chains 161 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 99 ASP Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 336 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.122534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.090454 restraints weight = 13551.656| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.09 r_work: 0.2951 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9081 Z= 0.221 Angle : 0.548 8.902 12304 Z= 0.274 Chirality : 0.041 0.175 1409 Planarity : 0.003 0.053 1551 Dihedral : 4.379 50.412 1300 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.85 % Allowed : 27.65 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1120 helix: 2.33 (0.27), residues: 382 sheet: 0.24 (0.30), residues: 285 loop : -0.98 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 109 HIS 0.006 0.001 HIS R 272 PHE 0.025 0.001 PHE R 182 TYR 0.023 0.001 TYR S 235 ARG 0.002 0.000 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2187.52 seconds wall clock time: 40 minutes 28.04 seconds (2428.04 seconds total)