Starting phenix.real_space_refine on Sun Apr 7 03:38:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3r_35965/04_2024/8j3r_35965.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3r_35965/04_2024/8j3r_35965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3r_35965/04_2024/8j3r_35965.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3r_35965/04_2024/8j3r_35965.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3r_35965/04_2024/8j3r_35965.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j3r_35965/04_2024/8j3r_35965.pdb" } resolution = 2.95 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 ------------------------------------------------------------------------------- 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= 0.010 sd= 0.076 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 140 5.49 5 Mg 3 5.21 5 S 32 5.16 5 C 5481 2.51 5 N 1731 2.21 5 O 2138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9526 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3429 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 10, 'TRANS': 411} Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 466 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "E" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "C" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2345 Classifications: {'RNA': 109} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 2, 'rna3p_pur': 56, 'rna3p_pyr': 41} Link IDs: {'rna2p': 12, 'rna3p': 96} Chain: "B" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3116 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 377} Chain breaks: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3055 SG CYS A 372 88.301 55.825 32.384 1.00103.10 S ATOM 3076 SG CYS A 375 91.722 54.642 33.836 1.00 97.25 S ATOM 3193 SG CYS A 391 90.472 58.181 34.340 1.00116.70 S ATOM 3215 SG CYS A 394 91.398 56.126 32.490 1.00100.31 S Time building chain proxies: 5.66, per 1000 atoms: 0.59 Number of scatterers: 9526 At special positions: 0 Unit cell: (102.3, 117.7, 113.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 32 16.00 P 140 15.00 Mg 3 11.99 O 2138 8.00 N 1731 7.00 C 5481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.02 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 394 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 391 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 372 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 375 " Number of angles added : 6 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1516 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 49.3% alpha, 17.6% beta 46 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 16 through 57 Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.628A pdb=" N TYR A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.638A pdb=" N ALA A 98 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 171 through 183 removed outlier: 4.060A pdb=" N THR A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 247 through 268 removed outlier: 3.759A pdb=" N GLU A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 279 through 284 removed outlier: 3.632A pdb=" N ARG A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 316 Processing helix chain 'A' and resid 341 through 356 removed outlier: 3.569A pdb=" N ALA A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 409 Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'B' and resid 16 through 46 Processing helix chain 'B' and resid 50 through 56 removed outlier: 4.153A pdb=" N ASP B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 81 removed outlier: 3.547A pdb=" N HIS B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 78 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 105 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 171 through 183 Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 286 through 317 Processing helix chain 'B' and resid 341 through 356 removed outlier: 3.553A pdb=" N GLU B 355 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 356 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 410 removed outlier: 3.808A pdb=" N ILE B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 420 removed outlier: 3.851A pdb=" N ALA B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.507A pdb=" N GLN A 191 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 200 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TRP A 201 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 166 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N SER A 164 " --> pdb=" O PRO A 12 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR A 142 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.507A pdb=" N GLN A 191 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 200 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 245 removed outlier: 3.521A pdb=" N ALA A 232 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N MET A 222 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLU A 324 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ILE A 224 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 321 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A 363 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N MET A 323 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 388 through 390 removed outlier: 3.638A pdb=" N ALA A 398 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.514A pdb=" N ALA B 189 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG B 208 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL B 187 " --> pdb=" O ARG B 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.756A pdb=" N ILE B 166 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N SER B 164 " --> pdb=" O PRO B 12 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR B 142 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 242 through 245 removed outlier: 7.169A pdb=" N LEU B 218 " --> pdb=" O CYS B 318 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B 320 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS B 220 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLN B 322 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N MET B 222 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N GLU B 324 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ILE B 224 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 388 through 390 356 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 212 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 5.06 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: 2190 1.33 - 1.45: 2776 1.45 - 1.57: 4700 1.57 - 1.69: 277 1.69 - 1.81: 54 Bond restraints: 9997 Sorted by residual: bond pdb=" CA ILE A 163 " pdb=" CB ILE A 163 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.11e-02 8.12e+03 1.19e+00 bond pdb=" CA ILE A 410 " pdb=" CB ILE A 410 " ideal model delta sigma weight residual 1.537 1.525 0.013 1.29e-02 6.01e+03 9.67e-01 bond pdb=" CB PRO B 365 " pdb=" CG PRO B 365 " ideal model delta sigma weight residual 1.492 1.539 -0.047 5.00e-02 4.00e+02 8.95e-01 bond pdb=" C1' DT E -7 " pdb=" N1 DT E -7 " ideal model delta sigma weight residual 1.490 1.518 -0.028 3.00e-02 1.11e+03 8.74e-01 bond pdb=" CB VAL A 10 " pdb=" CG2 VAL A 10 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.59e-01 ... (remaining 9992 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.70: 788 105.70 - 112.78: 5450 112.78 - 119.87: 3368 119.87 - 126.95: 4121 126.95 - 134.03: 416 Bond angle restraints: 14143 Sorted by residual: angle pdb=" C ARG A 197 " pdb=" N LYS A 198 " pdb=" CA LYS A 198 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.27e+00 angle pdb=" C1' U C -45 " pdb=" N1 U C -45 " pdb=" C2 U C -45 " ideal model delta sigma weight residual 117.70 125.34 -7.64 3.00e+00 1.11e-01 6.48e+00 angle pdb=" C2' U C 6 " pdb=" C1' U C 6 " pdb=" N1 U C 6 " ideal model delta sigma weight residual 112.00 115.56 -3.56 1.50e+00 4.44e-01 5.64e+00 angle pdb=" N GLN A 338 " pdb=" CA GLN A 338 " pdb=" C GLN A 338 " ideal model delta sigma weight residual 112.93 110.33 2.60 1.12e+00 7.97e-01 5.37e+00 angle pdb=" N ASN A 158 " pdb=" CA ASN A 158 " pdb=" CB ASN A 158 " ideal model delta sigma weight residual 113.65 110.33 3.32 1.47e+00 4.63e-01 5.11e+00 ... (remaining 14138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5076 17.90 - 35.80: 534 35.80 - 53.71: 264 53.71 - 71.61: 171 71.61 - 89.51: 33 Dihedral angle restraints: 6078 sinusoidal: 3711 harmonic: 2367 Sorted by residual: dihedral pdb=" CA LYS A 11 " pdb=" C LYS A 11 " pdb=" N PRO A 12 " pdb=" CA PRO A 12 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASN A 131 " pdb=" CB ASN A 131 " pdb=" CG ASN A 131 " pdb=" OD1 ASN A 131 " ideal model delta sinusoidal sigma weight residual 120.00 -168.80 -71.20 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP B 364 " pdb=" CB ASP B 364 " pdb=" CG ASP B 364 " pdb=" OD1 ASP B 364 " ideal model delta sinusoidal sigma weight residual -30.00 -86.06 56.06 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 6075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1234 0.035 - 0.069: 277 0.069 - 0.104: 87 0.104 - 0.138: 27 0.138 - 0.173: 3 Chirality restraints: 1628 Sorted by residual: chirality pdb=" C1' G C -83 " pdb=" O4' G C -83 " pdb=" C2' G C -83 " pdb=" N9 G C -83 " both_signs ideal model delta sigma weight residual False 2.46 2.28 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CA ILE A 116 " pdb=" N ILE A 116 " pdb=" C ILE A 116 " pdb=" CB ILE A 116 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" C1' U C -49 " pdb=" O4' U C -49 " pdb=" C2' U C -49 " pdb=" N1 U C -49 " both_signs ideal model delta sigma weight residual False 2.47 2.32 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 1625 not shown) Planarity restraints: 1293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U C 6 " -0.030 2.00e-02 2.50e+03 1.51e-02 5.12e+00 pdb=" N1 U C 6 " 0.032 2.00e-02 2.50e+03 pdb=" C2 U C 6 " 0.004 2.00e-02 2.50e+03 pdb=" O2 U C 6 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U C 6 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U C 6 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U C 6 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U C 6 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U C 6 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C -44 " -0.028 2.00e-02 2.50e+03 1.16e-02 4.04e+00 pdb=" N9 G C -44 " 0.026 2.00e-02 2.50e+03 pdb=" C8 G C -44 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G C -44 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G C -44 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C -44 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G C -44 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G C -44 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G C -44 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G C -44 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C -44 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G C -44 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 7 " -0.026 2.00e-02 2.50e+03 1.18e-02 3.86e+00 pdb=" N9 A C 7 " 0.028 2.00e-02 2.50e+03 pdb=" C8 A C 7 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A C 7 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A C 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A C 7 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A C 7 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A C 7 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A C 7 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A C 7 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A C 7 " -0.000 2.00e-02 2.50e+03 ... (remaining 1290 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 117 2.63 - 3.20: 7902 3.20 - 3.76: 16080 3.76 - 4.33: 22344 4.33 - 4.90: 33220 Nonbonded interactions: 79663 Sorted by model distance: nonbonded pdb=" OG SER A 334 " pdb="MG MG A 502 " model vdw 2.060 2.170 nonbonded pdb=" NE2 GLN B 322 " pdb=" O ILE B 408 " model vdw 2.229 2.520 nonbonded pdb=" O LEU B 337 " pdb=" OH TYR B 342 " model vdw 2.246 2.440 nonbonded pdb=" O2' U C -45 " pdb=" NZ LYS B 129 " model vdw 2.260 2.520 nonbonded pdb=" O2' A C -66 " pdb=" OE2 GLU B 108 " model vdw 2.266 2.440 ... (remaining 79658 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 58 or resid 65 through 81 or (resid 82 through 8 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 84 through 1 \ 60 or (resid 161 and (name N or name CA or name C or name O or name CB )) or res \ id 162 through 219 or (resid 220 and (name N or name CA or name C or name O or n \ ame CB )) or resid 221 through 224 or (resid 225 and (name N or name CA or name \ C or name O or name CB )) or resid 226 through 243 or (resid 244 and (name N or \ name CA or name C or name O or name CB )) or resid 245 through 257 or (resid 258 \ and (name N or name CA or name C or name O or name CB )) or resid 259 through 2 \ 65 or resid 285 through 326 or resid 331 or (resid 332 and (name N or name CA or \ name C or name O or name CB )) or resid 333 through 365 or (resid 366 and (name \ N or name CA or name C or name O or name CB )) or resid 367 through 378 or (res \ id 379 and (name N or name CA or name C or name O or name CB )) or resid 385 thr \ ough 414 or (resid 415 and (name N or name CA or name C or name O or name CB )) \ or resid 416 through 421)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.050 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 33.800 Find NCS groups from input model: 0.460 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:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4967 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 0.047 9997 Z= 0.158 Angle : 0.500 7.638 14143 Z= 0.288 Chirality : 0.036 0.173 1628 Planarity : 0.003 0.034 1293 Dihedral : 20.205 89.510 4562 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.46 % Allowed : 11.01 % Favored : 86.52 % 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: 0.87 (0.29), residues: 797 helix: 1.90 (0.26), residues: 361 sheet: 0.11 (0.39), residues: 162 loop : -0.90 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 43 HIS 0.003 0.001 HIS A 303 PHE 0.007 0.001 PHE B 102 TYR 0.011 0.001 TYR A 119 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASN cc_start: 0.6649 (OUTLIER) cc_final: 0.6447 (m110) REVERT: A 377 ASN cc_start: 0.6732 (t0) cc_final: 0.6497 (t0) REVERT: B 141 ASP cc_start: 0.6652 (OUTLIER) cc_final: 0.6234 (m-30) REVERT: B 142 TYR cc_start: 0.2634 (m-80) cc_final: 0.1486 (m-80) REVERT: B 288 GLU cc_start: 0.4753 (OUTLIER) cc_final: 0.4004 (tm-30) outliers start: 17 outliers final: 2 residues processed: 164 average time/residue: 1.3104 time to fit residues: 229.3055 Evaluate side-chains 113 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 320 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 HIS A 322 GLN A 407 ASN B 77 HIS B 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.9161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 9997 Z= 0.422 Angle : 0.882 12.846 14143 Z= 0.470 Chirality : 0.049 0.220 1628 Planarity : 0.007 0.059 1293 Dihedral : 22.032 88.382 2941 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.36 % Allowed : 16.81 % Favored : 77.83 % 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: -0.34 (0.27), residues: 797 helix: 0.80 (0.24), residues: 383 sheet: -0.52 (0.40), residues: 128 loop : -1.43 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP B 43 HIS 0.011 0.003 HIS A 139 PHE 0.021 0.004 PHE A 336 TYR 0.024 0.003 TYR A 119 ARG 0.010 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 234 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7603 (t0) cc_final: 0.7350 (t0) REVERT: A 82 LYS cc_start: 0.8484 (mttt) cc_final: 0.8196 (mttt) REVERT: A 233 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.8019 (t80) REVERT: A 351 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.6121 (t80) REVERT: B 126 ASP cc_start: 0.8333 (m-30) cc_final: 0.7794 (m-30) REVERT: B 147 SER cc_start: 0.8698 (OUTLIER) cc_final: 0.8497 (t) REVERT: B 196 ASP cc_start: 0.5905 (OUTLIER) cc_final: 0.5533 (p0) REVERT: B 355 GLU cc_start: 0.6383 (mt-10) cc_final: 0.6099 (mt-10) outliers start: 37 outliers final: 6 residues processed: 248 average time/residue: 1.4912 time to fit residues: 391.2567 Evaluate side-chains 198 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 188 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 320 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 87 ASN A 93 GLN A 131 ASN A 155 GLN A 194 HIS A 289 GLN A 347 GLN A 407 ASN B 87 ASN B 338 GLN B 403 ASN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 1.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9997 Z= 0.236 Angle : 0.603 8.984 14143 Z= 0.323 Chirality : 0.040 0.161 1628 Planarity : 0.004 0.046 1293 Dihedral : 21.794 88.470 2932 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 6.67 % Allowed : 25.22 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.29), residues: 797 helix: 2.03 (0.25), residues: 376 sheet: 0.01 (0.40), residues: 142 loop : -1.40 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 43 HIS 0.008 0.001 HIS A 278 PHE 0.013 0.002 PHE B 48 TYR 0.024 0.002 TYR B 233 ARG 0.013 0.001 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 199 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7716 (t0) cc_final: 0.7443 (t0) REVERT: A 29 GLN cc_start: 0.7807 (tp40) cc_final: 0.7547 (mm-40) REVERT: A 108 GLU cc_start: 0.8750 (mp0) cc_final: 0.8499 (mp0) REVERT: A 120 LYS cc_start: 0.8199 (pttt) cc_final: 0.7926 (pttt) REVERT: A 121 ARG cc_start: 0.7809 (ptm-80) cc_final: 0.7561 (ptm-80) REVERT: A 129 LYS cc_start: 0.9217 (ttmt) cc_final: 0.9002 (ttmm) REVERT: A 137 MET cc_start: 0.7978 (mmm) cc_final: 0.7677 (mmm) REVERT: A 182 SER cc_start: 0.8876 (OUTLIER) cc_final: 0.8604 (p) REVERT: A 220 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.6838 (mmtp) REVERT: A 261 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7741 (ttp80) REVERT: A 262 ILE cc_start: 0.8552 (mm) cc_final: 0.8159 (mm) REVERT: A 289 GLN cc_start: 0.8304 (tp40) cc_final: 0.8050 (tp40) REVERT: A 292 ASP cc_start: 0.7963 (t0) cc_final: 0.7739 (t0) REVERT: A 318 CYS cc_start: 0.8595 (m) cc_final: 0.8330 (m) REVERT: A 351 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6417 (t80) REVERT: A 359 LYS cc_start: 0.8116 (tttt) cc_final: 0.7900 (tttt) REVERT: A 366 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: B 6 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7443 (mtm-85) REVERT: B 118 SER cc_start: 0.8632 (t) cc_final: 0.8398 (p) REVERT: B 120 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8534 (tppp) REVERT: B 135 ASN cc_start: 0.8483 (m110) cc_final: 0.8279 (m110) REVERT: B 346 GLN cc_start: 0.7559 (tt0) cc_final: 0.6953 (mm110) outliers start: 46 outliers final: 10 residues processed: 221 average time/residue: 1.5522 time to fit residues: 362.2070 Evaluate side-chains 198 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 310 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 88 optimal weight: 0.0980 chunk 79 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 93 GLN A 131 ASN A 186 GLN A 347 GLN B 87 ASN B 256 GLN B 289 GLN B 303 HIS ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 1.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9997 Z= 0.188 Angle : 0.539 6.941 14143 Z= 0.292 Chirality : 0.038 0.152 1628 Planarity : 0.004 0.063 1293 Dihedral : 21.642 89.719 2931 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.23 % Allowed : 27.25 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.29), residues: 797 helix: 2.39 (0.26), residues: 377 sheet: 0.05 (0.38), residues: 161 loop : -1.19 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 45 HIS 0.006 0.001 HIS A 278 PHE 0.011 0.001 PHE B 236 TYR 0.029 0.001 TYR B 233 ARG 0.010 0.001 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 197 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7775 (t0) cc_final: 0.7521 (t0) REVERT: A 29 GLN cc_start: 0.7892 (tp40) cc_final: 0.7684 (mm-40) REVERT: A 50 SER cc_start: 0.8346 (m) cc_final: 0.8012 (t) REVERT: A 108 GLU cc_start: 0.8777 (mp0) cc_final: 0.8511 (mp0) REVERT: A 129 LYS cc_start: 0.9192 (ttmt) cc_final: 0.8974 (ttmm) REVERT: A 130 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7565 (tm-30) REVERT: A 137 MET cc_start: 0.8178 (mmm) cc_final: 0.7804 (mmm) REVERT: A 161 ARG cc_start: 0.7747 (mmm-85) cc_final: 0.7504 (mtp85) REVERT: A 182 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8712 (p) REVERT: A 230 VAL cc_start: 0.8538 (t) cc_final: 0.8316 (m) REVERT: A 261 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7983 (ttp80) REVERT: A 262 ILE cc_start: 0.8786 (mm) cc_final: 0.8497 (mm) REVERT: A 285 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7779 (tttp) REVERT: A 288 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7198 (tm-30) REVERT: A 318 CYS cc_start: 0.8692 (m) cc_final: 0.8376 (m) REVERT: A 351 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6610 (t80) REVERT: A 359 LYS cc_start: 0.8180 (tttt) cc_final: 0.7963 (tttt) REVERT: A 366 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: B 118 SER cc_start: 0.8650 (t) cc_final: 0.8376 (p) REVERT: B 120 LYS cc_start: 0.9000 (mmmm) cc_final: 0.8509 (tppp) REVERT: B 126 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: B 157 MET cc_start: 0.8210 (mpp) cc_final: 0.7664 (mpp) REVERT: B 196 ASP cc_start: 0.6437 (OUTLIER) cc_final: 0.6156 (p0) REVERT: B 233 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: B 346 GLN cc_start: 0.7734 (tt0) cc_final: 0.7148 (mm-40) REVERT: B 352 LYS cc_start: 0.8623 (mptm) cc_final: 0.8369 (mmtm) outliers start: 43 outliers final: 10 residues processed: 217 average time/residue: 1.4656 time to fit residues: 336.2522 Evaluate side-chains 199 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 310 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 10.0000 chunk 1 optimal weight: 0.0170 chunk 66 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 75 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.4624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 87 ASN A 93 GLN A 131 ASN A 186 GLN A 194 HIS A 346 GLN B 135 ASN B 303 HIS B 322 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 1.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9997 Z= 0.276 Angle : 0.602 7.521 14143 Z= 0.324 Chirality : 0.041 0.157 1628 Planarity : 0.005 0.052 1293 Dihedral : 21.581 84.401 2931 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.80 % Allowed : 28.26 % Favored : 65.94 % 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: 0.94 (0.29), residues: 797 helix: 2.17 (0.26), residues: 379 sheet: 0.00 (0.39), residues: 154 loop : -1.31 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 43 HIS 0.007 0.001 HIS A 278 PHE 0.013 0.002 PHE A 253 TYR 0.021 0.002 TYR B 7 ARG 0.008 0.001 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 199 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7802 (t0) cc_final: 0.7550 (t0) REVERT: A 29 GLN cc_start: 0.7904 (tp40) cc_final: 0.7696 (mm-40) REVERT: A 108 GLU cc_start: 0.8725 (mp0) cc_final: 0.8523 (mp0) REVERT: A 130 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7559 (tm-30) REVERT: A 137 MET cc_start: 0.8315 (mmm) cc_final: 0.8011 (mmm) REVERT: A 155 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8098 (mm-40) REVERT: A 240 PRO cc_start: 0.9367 (Cg_endo) cc_final: 0.9131 (Cg_exo) REVERT: A 261 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8129 (ttp80) REVERT: A 288 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7154 (tm-30) REVERT: A 299 ASP cc_start: 0.8684 (t0) cc_final: 0.8396 (t0) REVERT: A 318 CYS cc_start: 0.8827 (m) cc_final: 0.8525 (m) REVERT: A 351 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6578 (t80) REVERT: A 359 LYS cc_start: 0.8403 (tttt) cc_final: 0.8191 (tttt) REVERT: B 22 THR cc_start: 0.8755 (m) cc_final: 0.8501 (p) REVERT: B 118 SER cc_start: 0.8819 (t) cc_final: 0.8523 (p) REVERT: B 155 GLN cc_start: 0.7487 (tp-100) cc_final: 0.7223 (tp-100) REVERT: B 157 MET cc_start: 0.8284 (mpp) cc_final: 0.7878 (mpp) REVERT: B 178 ASP cc_start: 0.7486 (m-30) cc_final: 0.7130 (m-30) REVERT: B 233 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.7586 (t80) REVERT: B 262 ILE cc_start: 0.8686 (tp) cc_final: 0.8442 (tt) outliers start: 40 outliers final: 16 residues processed: 221 average time/residue: 1.5213 time to fit residues: 354.8501 Evaluate side-chains 206 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 324 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 21 optimal weight: 0.0050 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 186 GLN A 366 GLN B 135 ASN B 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 1.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9997 Z= 0.185 Angle : 0.535 6.811 14143 Z= 0.289 Chirality : 0.038 0.147 1628 Planarity : 0.004 0.067 1293 Dihedral : 21.546 80.587 2931 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.51 % Allowed : 30.58 % Favored : 63.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.29), residues: 797 helix: 2.51 (0.26), residues: 379 sheet: 0.10 (0.38), residues: 159 loop : -1.21 (0.34), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 45 HIS 0.004 0.001 HIS A 278 PHE 0.011 0.001 PHE A 253 TYR 0.013 0.001 TYR B 233 ARG 0.006 0.001 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 192 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6676 (pmm) cc_final: 0.6362 (mpp) REVERT: A 121 ARG cc_start: 0.7498 (ttp80) cc_final: 0.7226 (ttp-110) REVERT: A 130 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7524 (tm-30) REVERT: A 137 MET cc_start: 0.8242 (mmm) cc_final: 0.7960 (mmm) REVERT: A 155 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8099 (mm-40) REVERT: A 220 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7506 (mmtp) REVERT: A 261 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7936 (ttp80) REVERT: A 288 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7165 (tm-30) REVERT: A 291 ARG cc_start: 0.7479 (ttp-170) cc_final: 0.7268 (tpp80) REVERT: A 318 CYS cc_start: 0.8850 (m) cc_final: 0.8557 (m) REVERT: A 346 GLN cc_start: 0.8682 (mt0) cc_final: 0.8445 (mt0) REVERT: A 351 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6547 (t80) REVERT: A 420 SER cc_start: 0.7564 (m) cc_final: 0.7296 (p) REVERT: B 22 THR cc_start: 0.8679 (m) cc_final: 0.8436 (p) REVERT: B 39 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8669 (m) REVERT: B 114 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8702 (ptm) REVERT: B 118 SER cc_start: 0.8708 (t) cc_final: 0.8399 (p) REVERT: B 157 MET cc_start: 0.8255 (mpp) cc_final: 0.7869 (mpp) REVERT: B 178 ASP cc_start: 0.7465 (m-30) cc_final: 0.7098 (m-30) REVERT: B 199 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8274 (t0) REVERT: B 233 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7453 (t80) REVERT: B 262 ILE cc_start: 0.8736 (tp) cc_final: 0.8479 (tt) REVERT: B 346 GLN cc_start: 0.7696 (tt0) cc_final: 0.7312 (mm110) outliers start: 38 outliers final: 12 residues processed: 210 average time/residue: 1.6041 time to fit residues: 354.8367 Evaluate side-chains 211 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 192 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 199 ASN Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 363 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 88 optimal weight: 8.9990 chunk 55 optimal weight: 0.4980 chunk 54 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 186 GLN A 366 GLN A 370 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN B 194 HIS B 256 GLN B 322 GLN B 407 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 1.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9997 Z= 0.316 Angle : 0.608 7.436 14143 Z= 0.324 Chirality : 0.041 0.176 1628 Planarity : 0.005 0.073 1293 Dihedral : 21.627 85.701 2931 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.51 % Allowed : 31.30 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.29), residues: 797 helix: 2.25 (0.26), residues: 379 sheet: -0.02 (0.38), residues: 160 loop : -1.26 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 45 HIS 0.006 0.001 HIS A 278 PHE 0.011 0.002 PHE A 102 TYR 0.016 0.002 TYR B 402 ARG 0.007 0.001 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 203 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.7678 (ttp80) cc_final: 0.7466 (ttp80) REVERT: A 130 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7522 (tm-30) REVERT: A 141 ASP cc_start: 0.8174 (p0) cc_final: 0.7861 (p0) REVERT: A 155 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8085 (mm-40) REVERT: A 246 GLU cc_start: 0.7703 (mp0) cc_final: 0.7477 (mp0) REVERT: A 261 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8108 (ttp80) REVERT: A 270 TYR cc_start: 0.8459 (p90) cc_final: 0.7827 (p90) REVERT: A 288 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7179 (tm-30) REVERT: A 291 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6983 (mmm-85) REVERT: A 318 CYS cc_start: 0.8879 (m) cc_final: 0.8586 (m) REVERT: A 325 ASP cc_start: 0.7891 (t0) cc_final: 0.7651 (t0) REVERT: A 351 TYR cc_start: 0.7199 (OUTLIER) cc_final: 0.6471 (t80) REVERT: A 420 SER cc_start: 0.7766 (m) cc_final: 0.7461 (p) REVERT: B 118 SER cc_start: 0.8817 (t) cc_final: 0.8527 (p) REVERT: B 120 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8709 (tppp) REVERT: B 157 MET cc_start: 0.8317 (mpp) cc_final: 0.8046 (mpp) REVERT: B 177 MET cc_start: 0.8022 (mmt) cc_final: 0.7713 (mmt) REVERT: B 200 LYS cc_start: 0.8059 (mmmt) cc_final: 0.7786 (mmmt) REVERT: B 214 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6625 (ptp-110) REVERT: B 233 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7524 (t80) REVERT: B 262 ILE cc_start: 0.8763 (tp) cc_final: 0.8504 (tt) REVERT: B 315 LYS cc_start: 0.8351 (tttt) cc_final: 0.8014 (tttm) outliers start: 38 outliers final: 19 residues processed: 219 average time/residue: 1.5764 time to fit residues: 363.8709 Evaluate side-chains 225 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 201 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 324 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 139 HIS A 186 GLN A 256 GLN A 366 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 1.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9997 Z= 0.211 Angle : 0.557 7.042 14143 Z= 0.299 Chirality : 0.039 0.242 1628 Planarity : 0.004 0.056 1293 Dihedral : 21.613 80.925 2931 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.49 % Allowed : 33.62 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.29), residues: 797 helix: 2.43 (0.27), residues: 379 sheet: -0.05 (0.38), residues: 162 loop : -1.25 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 45 HIS 0.004 0.001 HIS A 278 PHE 0.010 0.001 PHE A 253 TYR 0.017 0.001 TYR B 243 ARG 0.006 0.001 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 206 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.7685 (ttp80) cc_final: 0.7420 (ttp80) REVERT: A 130 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7505 (tm-30) REVERT: A 155 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8090 (mm-40) REVERT: A 258 GLU cc_start: 0.8215 (tt0) cc_final: 0.7956 (tt0) REVERT: A 261 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8045 (ttp80) REVERT: A 266 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7051 (mtt180) REVERT: A 269 LYS cc_start: 0.8547 (pttt) cc_final: 0.8253 (pttm) REVERT: A 270 TYR cc_start: 0.8625 (p90) cc_final: 0.8038 (p90) REVERT: A 291 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7158 (tpp80) REVERT: A 299 ASP cc_start: 0.8578 (t0) cc_final: 0.8271 (t0) REVERT: A 318 CYS cc_start: 0.8912 (m) cc_final: 0.8641 (m) REVERT: A 351 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.6649 (t80) REVERT: A 420 SER cc_start: 0.7754 (m) cc_final: 0.7462 (p) REVERT: B 1 MET cc_start: 0.6851 (mtp) cc_final: 0.6442 (mmm) REVERT: B 118 SER cc_start: 0.8717 (t) cc_final: 0.8393 (p) REVERT: B 120 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8642 (tppp) REVERT: B 157 MET cc_start: 0.8317 (mpp) cc_final: 0.8076 (mpp) REVERT: B 200 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7823 (mmmt) REVERT: B 214 ARG cc_start: 0.6795 (ptp-110) cc_final: 0.6519 (ptp-110) REVERT: B 233 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7558 (t80) REVERT: B 262 ILE cc_start: 0.8777 (tp) cc_final: 0.8494 (tt) REVERT: B 291 ARG cc_start: 0.7087 (ttm110) cc_final: 0.6882 (ttm110) REVERT: B 416 ILE cc_start: 0.7965 (pp) cc_final: 0.7647 (mt) outliers start: 31 outliers final: 17 residues processed: 221 average time/residue: 1.5186 time to fit residues: 354.6169 Evaluate side-chains 213 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 324 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 1.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9997 Z= 0.272 Angle : 0.599 9.765 14143 Z= 0.318 Chirality : 0.040 0.175 1628 Planarity : 0.004 0.054 1293 Dihedral : 21.618 83.073 2931 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.77 % Allowed : 34.93 % Favored : 61.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.29), residues: 797 helix: 2.35 (0.26), residues: 379 sheet: -0.04 (0.38), residues: 160 loop : -1.28 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 45 HIS 0.004 0.001 HIS A 278 PHE 0.011 0.001 PHE A 253 TYR 0.019 0.002 TYR B 351 ARG 0.007 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 51 ASP cc_start: 0.7973 (m-30) cc_final: 0.7690 (m-30) REVERT: A 130 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 155 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8076 (mm-40) REVERT: A 258 GLU cc_start: 0.8276 (tt0) cc_final: 0.8015 (tt0) REVERT: A 261 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8085 (ttp80) REVERT: A 266 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7097 (mtt180) REVERT: A 269 LYS cc_start: 0.8563 (pttt) cc_final: 0.8311 (pttp) REVERT: A 270 TYR cc_start: 0.8487 (p90) cc_final: 0.8029 (p90) REVERT: A 318 CYS cc_start: 0.8911 (m) cc_final: 0.8650 (m) REVERT: A 351 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6485 (t80) REVERT: A 420 SER cc_start: 0.7809 (m) cc_final: 0.7534 (p) REVERT: B 118 SER cc_start: 0.8745 (t) cc_final: 0.8448 (p) REVERT: B 120 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8651 (tppp) REVERT: B 157 MET cc_start: 0.8301 (mpp) cc_final: 0.8092 (mpp) REVERT: B 200 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7852 (mmmt) REVERT: B 214 ARG cc_start: 0.7012 (ptp-110) cc_final: 0.6692 (ptp-110) REVERT: B 233 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.7561 (t80) REVERT: B 262 ILE cc_start: 0.8788 (tp) cc_final: 0.8507 (tt) REVERT: B 291 ARG cc_start: 0.7081 (ttm110) cc_final: 0.6877 (ttm110) REVERT: B 335 ARG cc_start: 0.7672 (mtt-85) cc_final: 0.7251 (mtt-85) REVERT: B 349 ILE cc_start: 0.7502 (mm) cc_final: 0.6992 (tt) outliers start: 26 outliers final: 17 residues processed: 199 average time/residue: 1.5995 time to fit residues: 334.9397 Evaluate side-chains 204 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 324 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 139 HIS A 366 GLN B 70 ASN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 1.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9997 Z= 0.180 Angle : 0.576 12.372 14143 Z= 0.305 Chirality : 0.038 0.209 1628 Planarity : 0.004 0.054 1293 Dihedral : 21.566 79.057 2931 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.77 % Allowed : 35.22 % Favored : 61.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.29), residues: 797 helix: 2.37 (0.26), residues: 380 sheet: -0.13 (0.37), residues: 162 loop : -1.24 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 45 HIS 0.003 0.001 HIS A 278 PHE 0.009 0.001 PHE A 253 TYR 0.029 0.001 TYR B 351 ARG 0.007 0.001 ARG A 280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8043 (m-30) cc_final: 0.7775 (m-30) REVERT: A 130 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 141 ASP cc_start: 0.8189 (p0) cc_final: 0.7986 (p0) REVERT: A 155 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8070 (mm-40) REVERT: A 228 VAL cc_start: 0.8512 (m) cc_final: 0.8280 (p) REVERT: A 258 GLU cc_start: 0.8229 (tt0) cc_final: 0.7945 (tt0) REVERT: A 261 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8022 (ttp80) REVERT: A 266 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6808 (mtt180) REVERT: A 269 LYS cc_start: 0.8546 (pttt) cc_final: 0.8203 (pttt) REVERT: A 318 CYS cc_start: 0.8900 (m) cc_final: 0.8656 (m) REVERT: A 351 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6719 (t80) REVERT: A 420 SER cc_start: 0.7721 (m) cc_final: 0.7445 (p) REVERT: B 114 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8697 (ptm) REVERT: B 118 SER cc_start: 0.8657 (t) cc_final: 0.8315 (p) REVERT: B 120 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8635 (tppp) REVERT: B 200 LYS cc_start: 0.8128 (mmmt) cc_final: 0.7841 (mmmt) REVERT: B 214 ARG cc_start: 0.7033 (ptp-110) cc_final: 0.6708 (ptp-110) REVERT: B 233 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7541 (t80) REVERT: B 291 ARG cc_start: 0.7038 (ttm110) cc_final: 0.6817 (ttm110) REVERT: B 335 ARG cc_start: 0.7637 (mtt-85) cc_final: 0.7284 (mtt-85) outliers start: 26 outliers final: 9 residues processed: 203 average time/residue: 1.5783 time to fit residues: 338.1645 Evaluate side-chains 198 residues out of total 700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 186 GLN A 256 GLN A 366 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 256 GLN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103433 restraints weight = 14570.033| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.87 r_work: 0.3179 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 1.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9997 Z= 0.227 Angle : 0.602 12.870 14143 Z= 0.314 Chirality : 0.039 0.192 1628 Planarity : 0.005 0.062 1293 Dihedral : 21.590 81.009 2931 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.32 % Allowed : 36.96 % Favored : 60.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.29), residues: 797 helix: 2.33 (0.26), residues: 380 sheet: -0.08 (0.37), residues: 160 loop : -1.32 (0.34), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 45 HIS 0.003 0.001 HIS A 238 PHE 0.009 0.001 PHE A 253 TYR 0.029 0.002 TYR B 351 ARG 0.016 0.001 ARG B 6 =============================================================================== Job complete usr+sys time: 5057.92 seconds wall clock time: 90 minutes 49.79 seconds (5449.79 seconds total)