Starting phenix.real_space_refine on Sat Dec 28 10:13:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0e_36762/12_2024/8k0e_36762.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0e_36762/12_2024/8k0e_36762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k0e_36762/12_2024/8k0e_36762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0e_36762/12_2024/8k0e_36762.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0e_36762/12_2024/8k0e_36762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0e_36762/12_2024/8k0e_36762.cif" } resolution = 3.65 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= 0.005 sd= 0.077 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 Fe 1 7.16 5 S 47 5.16 5 C 5273 2.51 5 N 1403 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8300 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5193 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 33, 'TRANS': 612} Chain breaks: 2 Chain: "B" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2994 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.91, per 1000 atoms: 0.59 Number of scatterers: 8300 At special positions: 0 Unit cell: (81.4, 105.6, 125.4, 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) Fe 1 26.01 S 47 16.00 O 1576 8.00 N 1403 7.00 C 5273 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 282 " 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 540 " " NAG D 1 " - " ASN A 316 " " NAG E 1 " - " ASN B 363 " " NAG F 1 " - " ASN B 87 " Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 971.6 milliseconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 3 sheets defined 65.2% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.746A pdb=" N LEU A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 83 removed outlier: 3.814A pdb=" N ALA A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 125 removed outlier: 3.692A pdb=" N GLY A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 removed outlier: 3.923A pdb=" N GLU A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.521A pdb=" N GLN A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 189 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.549A pdb=" N GLN A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.038A pdb=" N HIS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 281 removed outlier: 3.644A pdb=" N THR A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 285 Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 316 through 329 Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'A' and resid 349 through 356 removed outlier: 3.541A pdb=" N ILE A 356 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 384 Processing helix chain 'A' and resid 400 through 428 Processing helix chain 'A' and resid 441 through 447 Processing helix chain 'A' and resid 479 through 493 removed outlier: 3.578A pdb=" N CYS A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 528 Processing helix chain 'A' and resid 531 through 553 removed outlier: 3.862A pdb=" N ALA A 535 " --> pdb=" O PRO A 531 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 576 removed outlier: 3.863A pdb=" N GLN A 576 " --> pdb=" O GLU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 686 through 699 Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.864A pdb=" N GLU B 40 " --> pdb=" O PRO B 37 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 41 " --> pdb=" O ARG B 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 37 through 41' Processing helix chain 'B' and resid 43 through 57 Processing helix chain 'B' and resid 60 through 90 removed outlier: 3.776A pdb=" N CYS B 88 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER B 89 " --> pdb=" O HIS B 85 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 103 through 123 Processing helix chain 'B' and resid 124 through 125 No H-bonds generated for 'chain 'B' and resid 124 through 125' Processing helix chain 'B' and resid 126 through 131 removed outlier: 4.205A pdb=" N GLN B 131 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 144 Processing helix chain 'B' and resid 146 through 157 removed outlier: 4.200A pdb=" N PHE B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.820A pdb=" N LYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.729A pdb=" N SER B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 246 Proline residue: B 234 - end of helix Processing helix chain 'B' and resid 258 through 276 removed outlier: 4.427A pdb=" N HIS B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 308 Processing helix chain 'B' and resid 310 through 325 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.722A pdb=" N HIS B 341 " --> pdb=" O TYR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 352 removed outlier: 3.827A pdb=" N PHE B 352 " --> pdb=" O ASP B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 376 Processing sheet with id=AA1, first strand: chain 'A' and resid 458 through 461 removed outlier: 6.194A pdb=" N LEU A 459 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP A 475 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG A 647 " --> pdb=" O TYR A 617 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 673 " --> pdb=" O HIS A 565 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS A 565 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 563 " --> pdb=" O TRP A 675 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR A 677 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE A 561 " --> pdb=" O THR A 677 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 516 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 584 through 587 removed outlier: 6.223A pdb=" N VAL A 661 " --> pdb=" O PRO A 585 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 587 " --> pdb=" O HIS A 659 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE A 627 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU A 640 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE A 629 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 284 through 285 removed outlier: 4.194A pdb=" N ILE B 285 " --> pdb=" O TYR B 288 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1407 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: 2.21 Time building geometry restraints manager: 2.71 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: 1735 1.33 - 1.45: 2087 1.45 - 1.58: 4613 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 8505 Sorted by residual: bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.26e+00 ... (remaining 8500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 11437 3.30 - 6.60: 64 6.60 - 9.90: 9 9.90 - 13.20: 3 13.20 - 16.50: 2 Bond angle restraints: 11515 Sorted by residual: angle pdb=" CA LEU A 183 " pdb=" CB LEU A 183 " pdb=" CG LEU A 183 " ideal model delta sigma weight residual 116.30 132.80 -16.50 3.50e+00 8.16e-02 2.22e+01 angle pdb=" CB MET A 177 " pdb=" CG MET A 177 " pdb=" SD MET A 177 " ideal model delta sigma weight residual 112.70 126.80 -14.10 3.00e+00 1.11e-01 2.21e+01 angle pdb=" CA LEU A 445 " pdb=" CB LEU A 445 " pdb=" CG LEU A 445 " ideal model delta sigma weight residual 116.30 129.47 -13.17 3.50e+00 8.16e-02 1.41e+01 angle pdb=" CA LEU A 215 " pdb=" CB LEU A 215 " pdb=" CG LEU A 215 " ideal model delta sigma weight residual 116.30 128.23 -11.93 3.50e+00 8.16e-02 1.16e+01 angle pdb=" N GLY B 125 " pdb=" CA GLY B 125 " pdb=" C GLY B 125 " ideal model delta sigma weight residual 110.21 113.23 -3.02 9.10e-01 1.21e+00 1.10e+01 ... (remaining 11510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.71: 4638 24.71 - 49.42: 474 49.42 - 74.12: 69 74.12 - 98.83: 26 98.83 - 123.54: 18 Dihedral angle restraints: 5225 sinusoidal: 2237 harmonic: 2988 Sorted by residual: dihedral pdb=" CB CYS A 75 " pdb=" SG CYS A 75 " pdb=" SG CYS A 123 " pdb=" CB CYS A 123 " ideal model delta sinusoidal sigma weight residual 93.00 -178.25 -88.75 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS A 242 " pdb=" SG CYS A 242 " pdb=" SG CYS A 282 " pdb=" CB CYS A 282 " ideal model delta sinusoidal sigma weight residual 93.00 136.78 -43.78 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" C2 NAG C 1 " pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " pdb=" C5 NAG C 1 " ideal model delta sinusoidal sigma weight residual -62.96 60.58 -123.54 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 5222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 904 0.041 - 0.081: 243 0.081 - 0.122: 70 0.122 - 0.162: 6 0.162 - 0.203: 3 Chirality restraints: 1226 Sorted by residual: chirality pdb=" CG LEU A 138 " pdb=" CB LEU A 138 " pdb=" CD1 LEU A 138 " pdb=" CD2 LEU A 138 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA MET B 331 " pdb=" N MET B 331 " pdb=" C MET B 331 " pdb=" CB MET B 331 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.45e-01 chirality pdb=" CB THR A 34 " pdb=" CA THR A 34 " pdb=" OG1 THR A 34 " pdb=" CG2 THR A 34 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 1223 not shown) Planarity restraints: 1512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 94 " -0.061 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO A 95 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 604 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO A 605 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 657 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO A 658 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 658 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 658 " -0.022 5.00e-02 4.00e+02 ... (remaining 1509 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 125 2.66 - 3.22: 7857 3.22 - 3.78: 12732 3.78 - 4.34: 15006 4.34 - 4.90: 24964 Nonbonded interactions: 60684 Sorted by model distance: nonbonded pdb=" OH TYR A 312 " pdb=" OH TYR A 343 " model vdw 2.098 3.040 nonbonded pdb=" O TYR A 185 " pdb=" OG1 THR A 188 " model vdw 2.171 3.040 nonbonded pdb=" OG SER A 133 " pdb=" OE1 GLU A 135 " model vdw 2.187 3.040 nonbonded pdb=" O4 NAG D 2 " pdb=" O7 NAG D 2 " model vdw 2.192 3.040 nonbonded pdb=" OD2 ASP A 199 " pdb=" OG1 THR A 202 " model vdw 2.256 3.040 ... (remaining 60679 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.260 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 0.074 8505 Z= 0.226 Angle : 0.738 16.502 11515 Z= 0.360 Chirality : 0.041 0.203 1226 Planarity : 0.005 0.090 1508 Dihedral : 21.029 123.539 3297 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.12 % Allowed : 28.88 % Favored : 71.00 % 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: 1.22 (0.27), residues: 1000 helix: 2.07 (0.21), residues: 605 sheet: -0.25 (0.86), residues: 38 loop : -1.35 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 345 HIS 0.003 0.001 HIS B 351 PHE 0.018 0.001 PHE A 110 TYR 0.019 0.001 TYR B 338 ARG 0.006 0.001 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 1.013 Fit side-chains REVERT: A 471 ARG cc_start: 0.8378 (mtt90) cc_final: 0.7828 (mtt90) REVERT: A 696 MET cc_start: 0.8437 (ttm) cc_final: 0.8191 (ttm) REVERT: B 308 LEU cc_start: 0.8808 (tp) cc_final: 0.8494 (tp) outliers start: 1 outliers final: 1 residues processed: 108 average time/residue: 0.1731 time to fit residues: 27.9603 Evaluate side-chains 102 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 0.0170 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN B 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8505 Z= 0.219 Angle : 0.644 9.885 11515 Z= 0.317 Chirality : 0.041 0.198 1226 Planarity : 0.005 0.062 1508 Dihedral : 14.835 110.359 1301 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.53 % Allowed : 26.01 % Favored : 71.46 % 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: 1.51 (0.27), residues: 1000 helix: 2.25 (0.21), residues: 614 sheet: 0.11 (0.84), residues: 38 loop : -1.28 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 345 HIS 0.005 0.001 HIS A 481 PHE 0.015 0.001 PHE A 622 TYR 0.020 0.001 TYR B 338 ARG 0.003 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.968 Fit side-chains REVERT: A 234 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8161 (mp0) REVERT: A 444 ARG cc_start: 0.8918 (ttm170) cc_final: 0.8368 (mtt-85) REVERT: B 308 LEU cc_start: 0.8804 (tp) cc_final: 0.8504 (tp) outliers start: 22 outliers final: 10 residues processed: 122 average time/residue: 0.1592 time to fit residues: 29.3509 Evaluate side-chains 110 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8505 Z= 0.205 Angle : 0.610 9.020 11515 Z= 0.298 Chirality : 0.041 0.241 1226 Planarity : 0.004 0.059 1508 Dihedral : 13.154 108.870 1301 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.03 % Allowed : 25.20 % Favored : 70.77 % 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: 1.61 (0.27), residues: 1000 helix: 2.29 (0.21), residues: 620 sheet: 0.41 (0.73), residues: 48 loop : -1.29 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 345 HIS 0.005 0.001 HIS A 205 PHE 0.012 0.001 PHE A 331 TYR 0.015 0.001 TYR A 312 ARG 0.005 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.937 Fit side-chains REVERT: A 86 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7906 (pt0) REVERT: A 185 TYR cc_start: 0.9335 (t80) cc_final: 0.8939 (t80) REVERT: A 234 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: A 444 ARG cc_start: 0.9009 (ttm170) cc_final: 0.8702 (mtt-85) REVERT: B 308 LEU cc_start: 0.8779 (tp) cc_final: 0.8567 (tp) outliers start: 35 outliers final: 19 residues processed: 130 average time/residue: 0.1483 time to fit residues: 29.0639 Evaluate side-chains 123 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 366 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 54 optimal weight: 0.1980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8505 Z= 0.177 Angle : 0.605 9.389 11515 Z= 0.292 Chirality : 0.040 0.264 1226 Planarity : 0.004 0.058 1508 Dihedral : 12.438 108.349 1301 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.57 % Allowed : 25.78 % Favored : 70.66 % 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 (0.27), residues: 1000 helix: 2.30 (0.21), residues: 623 sheet: 0.57 (0.73), residues: 48 loop : -1.17 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 345 HIS 0.004 0.001 HIS A 205 PHE 0.011 0.001 PHE A 331 TYR 0.016 0.001 TYR A 312 ARG 0.003 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.960 Fit side-chains REVERT: A 86 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: A 185 TYR cc_start: 0.9356 (t80) cc_final: 0.8977 (t80) REVERT: A 234 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: A 444 ARG cc_start: 0.9035 (ttm170) cc_final: 0.8521 (mtt-85) REVERT: B 113 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7461 (tt) REVERT: B 308 LEU cc_start: 0.8780 (tp) cc_final: 0.8555 (tp) REVERT: B 345 TRP cc_start: 0.8691 (m-90) cc_final: 0.8452 (m-90) outliers start: 31 outliers final: 19 residues processed: 125 average time/residue: 0.1594 time to fit residues: 30.2961 Evaluate side-chains 121 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 380 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 0.0370 chunk 39 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.4980 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8505 Z= 0.152 Angle : 0.606 12.111 11515 Z= 0.289 Chirality : 0.040 0.276 1226 Planarity : 0.004 0.055 1508 Dihedral : 11.817 107.502 1301 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.22 % Allowed : 26.58 % Favored : 70.20 % 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 (0.27), residues: 1000 helix: 2.29 (0.21), residues: 624 sheet: 0.91 (0.75), residues: 49 loop : -1.08 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 345 HIS 0.004 0.001 HIS A 205 PHE 0.010 0.001 PHE B 256 TYR 0.016 0.001 TYR A 312 ARG 0.005 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.902 Fit side-chains REVERT: A 86 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7933 (pt0) REVERT: A 180 GLN cc_start: 0.9129 (tp40) cc_final: 0.8696 (tp-100) REVERT: A 185 TYR cc_start: 0.9382 (t80) cc_final: 0.9024 (t80) REVERT: A 234 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: A 444 ARG cc_start: 0.9022 (ttm170) cc_final: 0.8729 (mtt-85) REVERT: B 181 MET cc_start: 0.9409 (mmm) cc_final: 0.8992 (mmp) REVERT: B 308 LEU cc_start: 0.8732 (tp) cc_final: 0.8522 (tp) REVERT: B 345 TRP cc_start: 0.8661 (m-90) cc_final: 0.8423 (m-90) outliers start: 28 outliers final: 16 residues processed: 120 average time/residue: 0.1613 time to fit residues: 29.1718 Evaluate side-chains 115 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 380 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS A 657 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8505 Z= 0.177 Angle : 0.611 11.615 11515 Z= 0.291 Chirality : 0.040 0.289 1226 Planarity : 0.004 0.056 1508 Dihedral : 11.413 107.499 1301 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.37 % Allowed : 26.35 % Favored : 69.28 % 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: 1.81 (0.27), residues: 1000 helix: 2.28 (0.21), residues: 628 sheet: 1.03 (0.75), residues: 49 loop : -1.01 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 345 HIS 0.005 0.001 HIS A 205 PHE 0.011 0.001 PHE A 676 TYR 0.014 0.001 TYR B 337 ARG 0.005 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.971 Fit side-chains REVERT: A 37 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8315 (mm) REVERT: A 86 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7840 (pt0) REVERT: A 185 TYR cc_start: 0.9385 (t80) cc_final: 0.9033 (t80) REVERT: A 234 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: A 444 ARG cc_start: 0.9053 (ttm170) cc_final: 0.8624 (mtt-85) REVERT: B 113 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7503 (tt) REVERT: B 308 LEU cc_start: 0.8718 (tp) cc_final: 0.8503 (tp) REVERT: B 345 TRP cc_start: 0.8671 (m-90) cc_final: 0.8433 (m-90) outliers start: 38 outliers final: 20 residues processed: 129 average time/residue: 0.1682 time to fit residues: 32.1514 Evaluate side-chains 125 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 380 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS A 481 HIS A 536 HIS A 657 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8505 Z= 0.268 Angle : 0.652 8.529 11515 Z= 0.313 Chirality : 0.041 0.307 1226 Planarity : 0.004 0.058 1508 Dihedral : 11.129 108.497 1301 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.26 % Allowed : 26.47 % Favored : 69.28 % 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: 1.81 (0.27), residues: 1000 helix: 2.30 (0.21), residues: 626 sheet: 1.07 (0.76), residues: 49 loop : -1.04 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 345 HIS 0.016 0.001 HIS A 481 PHE 0.013 0.001 PHE A 676 TYR 0.014 0.001 TYR B 337 ARG 0.005 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 1.017 Fit side-chains REVERT: A 86 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7836 (pt0) REVERT: A 185 TYR cc_start: 0.9391 (t80) cc_final: 0.9066 (t80) REVERT: A 234 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: A 444 ARG cc_start: 0.9027 (ttm170) cc_final: 0.8637 (mtt-85) REVERT: B 113 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7602 (tt) REVERT: B 308 LEU cc_start: 0.8769 (tp) cc_final: 0.8541 (tp) REVERT: B 345 TRP cc_start: 0.8689 (m-90) cc_final: 0.8429 (m-90) outliers start: 37 outliers final: 27 residues processed: 123 average time/residue: 0.1641 time to fit residues: 30.4296 Evaluate side-chains 129 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 380 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8505 Z= 0.188 Angle : 0.639 12.821 11515 Z= 0.302 Chirality : 0.041 0.299 1226 Planarity : 0.004 0.056 1508 Dihedral : 10.816 106.684 1301 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.57 % Allowed : 27.04 % Favored : 69.39 % 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: 1.83 (0.27), residues: 1000 helix: 2.33 (0.21), residues: 625 sheet: 1.26 (0.84), residues: 39 loop : -1.02 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 345 HIS 0.004 0.001 HIS A 205 PHE 0.011 0.001 PHE A 676 TYR 0.016 0.001 TYR B 338 ARG 0.004 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.992 Fit side-chains REVERT: A 37 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8260 (mm) REVERT: A 86 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7826 (pt0) REVERT: A 185 TYR cc_start: 0.9400 (t80) cc_final: 0.9061 (t80) REVERT: A 234 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: A 444 ARG cc_start: 0.9005 (ttm170) cc_final: 0.8709 (mtt-85) REVERT: B 113 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7542 (tt) REVERT: B 308 LEU cc_start: 0.8723 (tp) cc_final: 0.8492 (tp) outliers start: 31 outliers final: 22 residues processed: 121 average time/residue: 0.1604 time to fit residues: 29.5930 Evaluate side-chains 126 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 380 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 9.9990 chunk 54 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS A 657 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8505 Z= 0.215 Angle : 0.644 14.246 11515 Z= 0.306 Chirality : 0.041 0.313 1226 Planarity : 0.004 0.056 1508 Dihedral : 10.496 106.896 1301 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.57 % Allowed : 27.16 % Favored : 69.28 % 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: 1.85 (0.27), residues: 1000 helix: 2.34 (0.21), residues: 626 sheet: 1.27 (0.84), residues: 39 loop : -1.01 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 345 HIS 0.004 0.001 HIS A 205 PHE 0.011 0.001 PHE A 676 TYR 0.012 0.001 TYR A 235 ARG 0.004 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.982 Fit side-chains REVERT: A 37 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8235 (mm) REVERT: A 86 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7824 (pt0) REVERT: A 185 TYR cc_start: 0.9403 (t80) cc_final: 0.9109 (t80) REVERT: A 234 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: A 347 MET cc_start: 0.8519 (tmm) cc_final: 0.8315 (tmm) REVERT: A 444 ARG cc_start: 0.9033 (ttm170) cc_final: 0.8538 (mtt-85) REVERT: A 491 ASN cc_start: 0.7916 (t0) cc_final: 0.7617 (t0) REVERT: B 113 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7585 (tt) REVERT: B 308 LEU cc_start: 0.8703 (tp) cc_final: 0.8483 (tp) outliers start: 31 outliers final: 23 residues processed: 123 average time/residue: 0.1581 time to fit residues: 29.4857 Evaluate side-chains 126 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 380 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8505 Z= 0.169 Angle : 0.646 14.263 11515 Z= 0.302 Chirality : 0.040 0.308 1226 Planarity : 0.004 0.055 1508 Dihedral : 10.288 107.203 1301 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.34 % Allowed : 27.96 % Favored : 68.70 % 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 (0.27), residues: 1000 helix: 2.32 (0.21), residues: 627 sheet: 1.36 (0.86), residues: 39 loop : -0.98 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 345 HIS 0.004 0.001 HIS A 205 PHE 0.008 0.001 PHE A 331 TYR 0.016 0.001 TYR A 312 ARG 0.004 0.000 ARG A 471 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.952 Fit side-chains REVERT: A 86 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7821 (pt0) REVERT: A 185 TYR cc_start: 0.9400 (t80) cc_final: 0.9100 (t80) REVERT: A 234 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: A 444 ARG cc_start: 0.8964 (ttm170) cc_final: 0.8627 (mtt-85) REVERT: A 491 ASN cc_start: 0.7911 (t0) cc_final: 0.7613 (t0) REVERT: B 308 LEU cc_start: 0.8655 (tp) cc_final: 0.8412 (tp) outliers start: 29 outliers final: 20 residues processed: 121 average time/residue: 0.1577 time to fit residues: 28.9024 Evaluate side-chains 123 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 234 GLU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 380 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.146501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.102879 restraints weight = 15617.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.106909 restraints weight = 9438.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.109612 restraints weight = 7013.084| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8505 Z= 0.169 Angle : 0.637 14.443 11515 Z= 0.297 Chirality : 0.040 0.314 1226 Planarity : 0.004 0.055 1508 Dihedral : 9.984 107.659 1301 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.99 % Allowed : 27.62 % Favored : 69.39 % 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: 1.95 (0.27), residues: 1000 helix: 2.35 (0.21), residues: 629 sheet: 1.36 (0.78), residues: 49 loop : -0.92 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 345 HIS 0.006 0.001 HIS A 481 PHE 0.013 0.001 PHE B 256 TYR 0.014 0.001 TYR B 337 ARG 0.004 0.000 ARG A 471 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1642.22 seconds wall clock time: 31 minutes 2.67 seconds (1862.67 seconds total)