Starting phenix.real_space_refine on Thu Nov 14 19:16:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8w_29857/11_2024/8g8w_29857_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8w_29857/11_2024/8g8w_29857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8w_29857/11_2024/8g8w_29857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8w_29857/11_2024/8g8w_29857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8w_29857/11_2024/8g8w_29857_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8w_29857/11_2024/8g8w_29857_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 23 5.16 5 C 4165 2.51 5 N 1066 2.21 5 O 1209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6471 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2146 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2814 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 24, 'TRANS': 373} Chain breaks: 5 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 10, 'GLU:plan': 16, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 169 Chain: "C" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1349 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 3 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 422 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 179 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 139 Unusual residues: {'CDL': 3, 'GTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 2, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 7.06, per 1000 atoms: 1.09 Number of scatterers: 6471 At special positions: 0 Unit cell: (72.24, 92.02, 203.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 8 15.00 O 1209 8.00 N 1066 7.00 C 4165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 98 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " GLC D 1 " - " GLC D 2 " Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 9 sheets defined 48.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 12 through 31 Processing helix chain 'A' and resid 31 through 43 removed outlier: 4.203A pdb=" N ASP A 35 " --> pdb=" O THR A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 70 removed outlier: 3.549A pdb=" N GLY A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 88 through 105 removed outlier: 4.341A pdb=" N ASP A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 130 Processing helix chain 'A' and resid 131 through 144 removed outlier: 4.109A pdb=" N GLU A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 176 through 205 removed outlier: 3.890A pdb=" N ASN A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 242 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 270 through 298 removed outlier: 4.158A pdb=" N LYS A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.931A pdb=" N ASN B 34 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR B 35 " --> pdb=" O LEU B 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 31 through 35' Processing helix chain 'B' and resid 65 through 68 removed outlier: 4.044A pdb=" N GLU B 68 " --> pdb=" O ASP B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.882A pdb=" N THR B 94 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 153 removed outlier: 3.594A pdb=" N LEU B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 172 Proline residue: B 169 - end of helix Processing helix chain 'B' and resid 185 through 195 removed outlier: 4.219A pdb=" N GLY B 189 " --> pdb=" O HIS B 185 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 211 through 217 Processing helix chain 'B' and resid 274 through 277 Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.740A pdb=" N ILE B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 359 Processing helix chain 'B' and resid 393 through 404 Processing helix chain 'B' and resid 407 through 418 removed outlier: 3.966A pdb=" N ASP B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS B 418 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 433 removed outlier: 3.650A pdb=" N GLU B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.518A pdb=" N LYS B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.614A pdb=" N PHE B 460 " --> pdb=" O GLN B 456 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B 461 " --> pdb=" O MET B 457 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR B 462 " --> pdb=" O SER B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 35 removed outlier: 3.515A pdb=" N TYR C 35 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 109 through 114 removed outlier: 3.532A pdb=" N TYR C 112 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'C' and resid 167 through 172 removed outlier: 3.594A pdb=" N PHE C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 408 removed outlier: 3.602A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.723A pdb=" N GLY B 13 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET B 37 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 52 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG B 41 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N PHE B 50 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 156 through 159 removed outlier: 6.496A pdb=" N LEU B 128 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLU B 159 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE B 130 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA B 385 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AA5, first strand: chain 'B' and resid 346 through 348 Processing sheet with id=AA6, first strand: chain 'C' and resid 8 through 10 Processing sheet with id=AA7, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.813A pdb=" N GLY C 13 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG C 41 " --> pdb=" O PHE C 50 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE C 50 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.813A pdb=" N GLY C 13 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 120 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 162 through 163 removed outlier: 7.536A pdb=" N ILE C 134 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU C 387 " --> pdb=" O ILE C 233 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1017 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: 2.15 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1069 1.32 - 1.45: 1808 1.45 - 1.57: 3699 1.57 - 1.69: 15 1.69 - 1.82: 36 Bond restraints: 6627 Sorted by residual: bond pdb=" OA3 CDL A 402 " pdb=" PA1 CDL A 402 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.64e+00 bond pdb=" OB3 CDL A 404 " pdb=" PB2 CDL A 404 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.51e+00 bond pdb=" OB3 CDL A 403 " pdb=" PB2 CDL A 403 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.35e+00 bond pdb=" OA3 CDL A 404 " pdb=" PA1 CDL A 404 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.26e+00 bond pdb=" OA3 CDL A 403 " pdb=" PA1 CDL A 403 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.03e+00 ... (remaining 6622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 8949 2.52 - 5.04: 101 5.04 - 7.57: 18 7.57 - 10.09: 8 10.09 - 12.61: 3 Bond angle restraints: 9079 Sorted by residual: angle pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sigma weight residual 120.50 133.11 -12.61 3.00e+00 1.11e-01 1.77e+01 angle pdb=" C1' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C3' GTP A 401 " ideal model delta sigma weight residual 111.00 99.26 11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O1B GTP A 401 " pdb=" PB GTP A 401 " pdb=" O2B GTP A 401 " ideal model delta sigma weight residual 109.50 119.63 -10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" CB MET B 442 " pdb=" CG MET B 442 " pdb=" SD MET B 442 " ideal model delta sigma weight residual 112.70 122.34 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" PB GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sigma weight residual 120.50 130.08 -9.58 3.00e+00 1.11e-01 1.02e+01 ... (remaining 9074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 3739 35.44 - 70.89: 115 70.89 - 106.33: 5 106.33 - 141.77: 2 141.77 - 177.22: 2 Dihedral angle restraints: 3863 sinusoidal: 1294 harmonic: 2569 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -78.19 -177.22 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual -68.92 83.42 -152.34 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual 303.79 171.36 132.44 1 2.00e+01 2.50e-03 4.02e+01 ... (remaining 3860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 935 0.070 - 0.140: 100 0.140 - 0.210: 4 0.210 - 0.280: 0 0.280 - 0.350: 4 Chirality restraints: 1043 Sorted by residual: chirality pdb=" C1 GLC D 1 " pdb=" C2 GLC D 1 " pdb=" O1 GLC D 1 " pdb=" O5 GLC D 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.39 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" C3' GTP A 401 " pdb=" C2' GTP A 401 " pdb=" C4' GTP A 401 " pdb=" O3' GTP A 401 " both_signs ideal model delta sigma weight residual False -2.47 -2.78 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA4 CDL A 402 " pdb=" CA3 CDL A 402 " pdb=" CA6 CDL A 402 " pdb=" OA6 CDL A 402 " both_signs ideal model delta sigma weight residual False -2.57 -2.27 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 1040 not shown) Planarity restraints: 1152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 89 " 0.043 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO C 90 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 231 " 0.031 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO C 232 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 232 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 232 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 454 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 455 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 455 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 455 " 0.020 5.00e-02 4.00e+02 ... (remaining 1149 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1151 2.77 - 3.30: 5841 3.30 - 3.83: 10176 3.83 - 4.37: 10576 4.37 - 4.90: 19789 Nonbonded interactions: 47533 Sorted by model distance: nonbonded pdb=" OG SER C 55 " pdb=" OH TYR C 112 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASP B 179 " pdb=" OG SER B 391 " model vdw 2.238 3.040 nonbonded pdb=" NE2 GLN A 42 " pdb=" OD2 ASP A 234 " model vdw 2.309 3.120 nonbonded pdb=" O ASP C 75 " pdb=" N ASN C 79 " model vdw 2.316 3.120 nonbonded pdb=" NZ LYS A 138 " pdb=" O1B GTP A 401 " model vdw 2.324 3.120 ... (remaining 47528 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.220 Find NCS groups from input model: 0.070 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6627 Z= 0.266 Angle : 0.686 12.609 9079 Z= 0.315 Chirality : 0.046 0.350 1043 Planarity : 0.004 0.066 1152 Dihedral : 17.422 177.216 2215 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.18 % Allowed : 19.37 % Favored : 80.44 % 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: 1.75 (0.29), residues: 880 helix: 2.73 (0.28), residues: 344 sheet: 0.79 (0.40), residues: 144 loop : -0.10 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 281 HIS 0.002 0.001 HIS A 146 PHE 0.008 0.001 PHE A 286 TYR 0.011 0.001 TYR C 82 ARG 0.002 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.719 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.1658 time to fit residues: 13.0110 Evaluate side-chains 50 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 26 optimal weight: 0.0670 chunk 41 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6627 Z= 0.183 Angle : 0.514 7.841 9079 Z= 0.256 Chirality : 0.041 0.178 1043 Planarity : 0.004 0.055 1152 Dihedral : 14.045 177.565 1094 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.48 % Allowed : 18.27 % Favored : 80.26 % 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: 1.86 (0.29), residues: 880 helix: 2.71 (0.28), residues: 361 sheet: 0.84 (0.40), residues: 143 loop : -0.06 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 281 HIS 0.002 0.001 HIS B 185 PHE 0.007 0.001 PHE B 182 TYR 0.008 0.001 TYR B 227 ARG 0.004 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.630 Fit side-chains REVERT: A 292 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8505 (tt) outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 0.1587 time to fit residues: 13.8388 Evaluate side-chains 53 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 237 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN B 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 6627 Z= 0.425 Angle : 0.636 7.222 9079 Z= 0.328 Chirality : 0.045 0.184 1043 Planarity : 0.005 0.059 1152 Dihedral : 13.661 177.202 1094 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.06 % Allowed : 16.61 % Favored : 79.34 % 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: 1.32 (0.28), residues: 880 helix: 2.26 (0.27), residues: 357 sheet: 0.70 (0.41), residues: 139 loop : -0.37 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 39 HIS 0.004 0.001 HIS B 160 PHE 0.017 0.002 PHE A 224 TYR 0.015 0.002 TYR C 97 ARG 0.005 0.001 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 155 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8714 (m) REVERT: A 168 GLU cc_start: 0.7982 (tp30) cc_final: 0.7705 (tp30) outliers start: 22 outliers final: 13 residues processed: 68 average time/residue: 0.1494 time to fit residues: 14.8830 Evaluate side-chains 62 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.0670 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6627 Z= 0.192 Angle : 0.524 6.637 9079 Z= 0.262 Chirality : 0.041 0.163 1043 Planarity : 0.004 0.053 1152 Dihedral : 13.191 179.538 1094 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.21 % Allowed : 18.63 % Favored : 79.15 % 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: 1.63 (0.29), residues: 880 helix: 2.55 (0.28), residues: 358 sheet: 0.72 (0.40), residues: 139 loop : -0.18 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 281 HIS 0.002 0.001 HIS A 146 PHE 0.008 0.001 PHE A 224 TYR 0.009 0.001 TYR B 227 ARG 0.003 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 155 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8640 (m) REVERT: A 168 GLU cc_start: 0.7818 (tp30) cc_final: 0.7539 (tp30) REVERT: B 30 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7321 (pp) REVERT: C 10 SER cc_start: 0.6527 (m) cc_final: 0.6015 (t) outliers start: 12 outliers final: 6 residues processed: 65 average time/residue: 0.1582 time to fit residues: 15.0275 Evaluate side-chains 59 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6627 Z= 0.251 Angle : 0.545 6.607 9079 Z= 0.274 Chirality : 0.042 0.168 1043 Planarity : 0.005 0.052 1152 Dihedral : 13.050 176.699 1094 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.32 % Allowed : 17.16 % Favored : 79.52 % 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: 1.59 (0.29), residues: 880 helix: 2.55 (0.27), residues: 358 sheet: 0.60 (0.39), residues: 143 loop : -0.21 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 56 HIS 0.002 0.001 HIS B 160 PHE 0.010 0.001 PHE A 224 TYR 0.009 0.001 TYR B 98 ARG 0.004 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 155 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8628 (m) REVERT: A 168 GLU cc_start: 0.7887 (tp30) cc_final: 0.7656 (tp30) REVERT: A 285 MET cc_start: 0.7895 (tmm) cc_final: 0.7445 (tmm) REVERT: B 30 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7333 (pp) REVERT: C 10 SER cc_start: 0.6530 (m) cc_final: 0.6024 (t) outliers start: 18 outliers final: 10 residues processed: 68 average time/residue: 0.1500 time to fit residues: 14.8091 Evaluate side-chains 62 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 0.0870 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 82 optimal weight: 0.0000 overall best weight: 0.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6627 Z= 0.179 Angle : 0.512 6.684 9079 Z= 0.255 Chirality : 0.041 0.159 1043 Planarity : 0.004 0.050 1152 Dihedral : 12.626 175.499 1094 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.40 % Allowed : 18.63 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.29), residues: 880 helix: 2.67 (0.27), residues: 358 sheet: 0.72 (0.39), residues: 143 loop : -0.08 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 56 HIS 0.001 0.001 HIS B 160 PHE 0.006 0.001 PHE C 40 TYR 0.009 0.001 TYR B 227 ARG 0.003 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 155 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8586 (m) REVERT: A 168 GLU cc_start: 0.7769 (tp30) cc_final: 0.7524 (tp30) REVERT: B 30 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7253 (pp) REVERT: B 186 ASP cc_start: 0.8339 (p0) cc_final: 0.8092 (p0) REVERT: C 10 SER cc_start: 0.6513 (m) cc_final: 0.6008 (t) outliers start: 13 outliers final: 10 residues processed: 63 average time/residue: 0.1512 time to fit residues: 13.9771 Evaluate side-chains 61 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6627 Z= 0.240 Angle : 0.538 6.637 9079 Z= 0.270 Chirality : 0.041 0.167 1043 Planarity : 0.004 0.051 1152 Dihedral : 12.529 175.863 1094 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.77 % Allowed : 19.19 % Favored : 78.04 % 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: 1.70 (0.29), residues: 880 helix: 2.65 (0.27), residues: 357 sheet: 0.69 (0.39), residues: 143 loop : -0.16 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 279 HIS 0.002 0.001 HIS B 160 PHE 0.008 0.001 PHE A 224 TYR 0.009 0.001 TYR B 227 ARG 0.003 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.703 Fit side-chains REVERT: A 155 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8626 (m) REVERT: A 168 GLU cc_start: 0.7898 (tp30) cc_final: 0.7637 (tp30) REVERT: A 285 MET cc_start: 0.7892 (tmm) cc_final: 0.7384 (tmm) REVERT: B 30 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7362 (pp) REVERT: B 106 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7374 (t80) REVERT: B 186 ASP cc_start: 0.8352 (p0) cc_final: 0.8089 (p0) REVERT: C 10 SER cc_start: 0.6538 (m) cc_final: 0.6054 (t) outliers start: 15 outliers final: 12 residues processed: 64 average time/residue: 0.1512 time to fit residues: 14.1240 Evaluate side-chains 64 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 21 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6627 Z= 0.239 Angle : 0.545 6.647 9079 Z= 0.273 Chirality : 0.041 0.163 1043 Planarity : 0.004 0.050 1152 Dihedral : 12.122 175.445 1094 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.51 % Allowed : 18.63 % Favored : 77.86 % 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: 1.68 (0.29), residues: 880 helix: 2.63 (0.27), residues: 358 sheet: 0.70 (0.39), residues: 143 loop : -0.18 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 56 HIS 0.002 0.001 HIS B 160 PHE 0.008 0.001 PHE A 224 TYR 0.009 0.001 TYR C 97 ARG 0.003 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.775 Fit side-chains REVERT: A 101 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7448 (tm-30) REVERT: A 155 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8635 (m) REVERT: A 168 GLU cc_start: 0.8050 (tp30) cc_final: 0.7796 (tp30) REVERT: A 285 MET cc_start: 0.7869 (tmm) cc_final: 0.7354 (tmm) REVERT: B 30 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7405 (pp) REVERT: B 106 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7335 (t80) REVERT: C 10 SER cc_start: 0.6519 (m) cc_final: 0.6060 (t) outliers start: 19 outliers final: 12 residues processed: 67 average time/residue: 0.1557 time to fit residues: 15.3415 Evaluate side-chains 64 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain C residue 15 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.8073 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6627 Z= 0.209 Angle : 0.539 7.338 9079 Z= 0.267 Chirality : 0.041 0.163 1043 Planarity : 0.004 0.050 1152 Dihedral : 11.727 174.065 1094 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.14 % Allowed : 19.19 % Favored : 77.68 % 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: 1.73 (0.29), residues: 880 helix: 2.68 (0.28), residues: 358 sheet: 0.71 (0.39), residues: 143 loop : -0.16 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 56 HIS 0.002 0.001 HIS B 160 PHE 0.007 0.001 PHE A 224 TYR 0.009 0.001 TYR B 227 ARG 0.003 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.693 Fit side-chains REVERT: A 155 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8634 (m) REVERT: A 168 GLU cc_start: 0.8024 (tp30) cc_final: 0.7777 (tp30) REVERT: B 30 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7326 (pp) REVERT: B 106 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7350 (t80) REVERT: C 10 SER cc_start: 0.6505 (m) cc_final: 0.5952 (t) REVERT: C 70 PHE cc_start: 0.8408 (m-80) cc_final: 0.8099 (m-80) outliers start: 17 outliers final: 14 residues processed: 68 average time/residue: 0.1511 time to fit residues: 15.1153 Evaluate side-chains 68 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain C residue 15 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.0870 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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: 0.8093 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6627 Z= 0.242 Angle : 0.561 8.487 9079 Z= 0.279 Chirality : 0.041 0.167 1043 Planarity : 0.004 0.051 1152 Dihedral : 11.425 174.521 1094 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.14 % Allowed : 19.37 % Favored : 77.49 % 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: 1.64 (0.29), residues: 880 helix: 2.58 (0.28), residues: 359 sheet: 0.64 (0.39), residues: 143 loop : -0.18 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 351 HIS 0.002 0.001 HIS B 160 PHE 0.008 0.001 PHE A 224 TYR 0.010 0.001 TYR B 227 ARG 0.003 0.000 ARG C 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.720 Fit side-chains REVERT: A 101 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7405 (tm-30) REVERT: A 155 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8629 (m) REVERT: A 168 GLU cc_start: 0.8113 (tp30) cc_final: 0.7873 (tp30) REVERT: A 285 MET cc_start: 0.7886 (tmm) cc_final: 0.7447 (tmm) REVERT: B 30 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7363 (pp) REVERT: B 106 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.7352 (t80) REVERT: B 186 ASP cc_start: 0.8308 (p0) cc_final: 0.8010 (p0) REVERT: C 10 SER cc_start: 0.6410 (m) cc_final: 0.5975 (t) REVERT: C 70 PHE cc_start: 0.8394 (m-80) cc_final: 0.8115 (m-80) outliers start: 17 outliers final: 13 residues processed: 65 average time/residue: 0.1554 time to fit residues: 14.6118 Evaluate side-chains 64 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 454 ILE Chi-restraints excluded: chain C residue 15 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 29 optimal weight: 0.0030 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 61 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 403 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.156243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.3740 r_free = 0.3740 target = 0.136700 restraints weight = 10597.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133197 restraints weight = 13110.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133770 restraints weight = 11669.051| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6627 Z= 0.175 Angle : 0.529 9.024 9079 Z= 0.261 Chirality : 0.040 0.157 1043 Planarity : 0.004 0.049 1152 Dihedral : 11.021 173.646 1094 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.40 % Allowed : 20.11 % Favored : 77.49 % 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: 1.77 (0.29), residues: 880 helix: 2.67 (0.28), residues: 360 sheet: 0.67 (0.39), residues: 143 loop : -0.07 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 281 HIS 0.001 0.000 HIS B 160 PHE 0.006 0.001 PHE C 40 TYR 0.015 0.001 TYR C 82 ARG 0.012 0.000 ARG C 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1712.48 seconds wall clock time: 31 minutes 58.66 seconds (1918.66 seconds total)