Starting phenix.real_space_refine on Wed Sep 17 08:43:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nei_49311/09_2025/9nei_49311.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nei_49311/09_2025/9nei_49311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nei_49311/09_2025/9nei_49311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nei_49311/09_2025/9nei_49311.map" model { file = "/net/cci-nas-00/data/ceres_data/9nei_49311/09_2025/9nei_49311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nei_49311/09_2025/9nei_49311.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.038 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 K 2 8.98 5 S 29 5.16 5 C 4848 2.51 5 N 1032 2.21 5 O 1145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7056 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1654 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1648 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1654 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1647 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 98 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 82 Unusual residues: {' K': 1, 'POV': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-1': 6, 'POV:plan-2': 5, 'POV:plan-3': 5} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 102 Unusual residues: {' K': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 7} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 95 Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-1': 8, 'POV:plan-2': 7, 'POV:plan-3': 7} Unresolved non-hydrogen planarities: 77 Chain: "D" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7, 'water': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 289 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 5} Unresolved non-hydrogen planarities: 63 Time building chain proxies: 1.91, per 1000 atoms: 0.27 Number of scatterers: 7056 At special positions: 0 Unit cell: (107.07, 107.9, 67.23, 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) K 2 19.00 S 29 16.00 O 1145 8.00 N 1032 7.00 C 4848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 356.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1614 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 224 through 248 removed outlier: 3.539A pdb=" N VAL A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 298 Processing helix chain 'A' and resid 311 through 327 removed outlier: 3.847A pdb=" N ILE A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 3.779A pdb=" N LEU A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 379 through 392 removed outlier: 3.522A pdb=" N GLN A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 419 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 452 through 471 Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.758A pdb=" N ILE A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 248 Processing helix chain 'B' and resid 278 through 298 Processing helix chain 'B' and resid 311 through 326 removed outlier: 3.839A pdb=" N ILE B 320 " --> pdb=" O ASP B 316 " (cutoff:3.500A) Proline residue: B 322 - end of helix Processing helix chain 'B' and resid 358 through 368 Processing helix chain 'B' and resid 369 through 378 Processing helix chain 'B' and resid 379 through 392 removed outlier: 3.501A pdb=" N GLN B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 419 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 441 Processing helix chain 'B' and resid 452 through 472 Processing helix chain 'B' and resid 473 through 489 removed outlier: 3.660A pdb=" N ILE B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 489 " --> pdb=" O TYR B 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 248 removed outlier: 4.132A pdb=" N VAL C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 298 removed outlier: 3.520A pdb=" N ILE C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 327 removed outlier: 3.774A pdb=" N ILE C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Proline residue: C 322 - end of helix removed outlier: 3.607A pdb=" N LEU C 327 " --> pdb=" O TYR C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 379 through 392 Processing helix chain 'C' and resid 392 through 419 Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 441 Processing helix chain 'C' and resid 452 through 472 Processing helix chain 'C' and resid 473 through 488 removed outlier: 3.859A pdb=" N ILE C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 248 Processing helix chain 'D' and resid 278 through 298 removed outlier: 3.531A pdb=" N ILE D 282 " --> pdb=" O PRO D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 327 removed outlier: 3.783A pdb=" N ILE D 320 " --> pdb=" O ASP D 316 " (cutoff:3.500A) Proline residue: D 322 - end of helix removed outlier: 3.610A pdb=" N LEU D 327 " --> pdb=" O TYR D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 369 through 378 Processing helix chain 'D' and resid 379 through 392 removed outlier: 3.650A pdb=" N GLN D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 419 Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 441 Processing helix chain 'D' and resid 452 through 472 Processing helix chain 'D' and resid 473 through 489 removed outlier: 3.759A pdb=" N ILE D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 14 501 hydrogen bonds defined for protein. 1413 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: 1.03 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 999 1.31 - 1.43: 1963 1.43 - 1.56: 4092 1.56 - 1.68: 84 1.68 - 1.81: 46 Bond restraints: 7184 Sorted by residual: bond pdb=" C31 POV A 702 " pdb=" O31 POV A 702 " ideal model delta sigma weight residual 1.327 1.443 -0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C31 POV C 702 " pdb=" O31 POV C 702 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C31 POV B 702 " pdb=" O31 POV B 702 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C31 POV D 701 " pdb=" O31 POV D 701 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C31 POV D 702 " pdb=" O31 POV D 702 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.28e+01 ... (remaining 7179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 9286 2.34 - 4.68: 236 4.68 - 7.01: 98 7.01 - 9.35: 24 9.35 - 11.69: 5 Bond angle restraints: 9649 Sorted by residual: angle pdb=" CA THR A 469 " pdb=" CB THR A 469 " pdb=" OG1 THR A 469 " ideal model delta sigma weight residual 109.60 104.48 5.12 1.50e+00 4.44e-01 1.16e+01 angle pdb=" N ARG A 487 " pdb=" CA ARG A 487 " pdb=" C ARG A 487 " ideal model delta sigma weight residual 111.14 107.51 3.63 1.08e+00 8.57e-01 1.13e+01 angle pdb=" C32 POV A 702 " pdb=" C31 POV A 702 " pdb=" O31 POV A 702 " ideal model delta sigma weight residual 110.66 120.73 -10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CA LEU G 12 " pdb=" CB LEU G 12 " pdb=" CG LEU G 12 " ideal model delta sigma weight residual 116.30 127.99 -11.69 3.50e+00 8.16e-02 1.12e+01 angle pdb=" C32 POV B 702 " pdb=" C31 POV B 702 " pdb=" O31 POV B 702 " ideal model delta sigma weight residual 110.66 120.51 -9.85 3.00e+00 1.11e-01 1.08e+01 ... (remaining 9644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.55: 3752 19.55 - 39.10: 318 39.10 - 58.65: 97 58.65 - 78.20: 7 78.20 - 97.75: 3 Dihedral angle restraints: 4177 sinusoidal: 1701 harmonic: 2476 Sorted by residual: dihedral pdb=" CA THR G 2 " pdb=" C THR G 2 " pdb=" N MET G 3 " pdb=" CA MET G 3 " ideal model delta harmonic sigma weight residual 180.00 157.09 22.91 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" C3 POV A 702 " pdb=" C31 POV A 702 " pdb=" O31 POV A 702 " pdb=" C32 POV A 702 " ideal model delta sinusoidal sigma weight residual 172.61 74.86 97.75 1 3.00e+01 1.11e-03 1.21e+01 dihedral pdb=" CA MET G 3 " pdb=" C MET G 3 " pdb=" N ALA G 4 " pdb=" CA ALA G 4 " ideal model delta harmonic sigma weight residual 180.00 162.91 17.09 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 4174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 844 0.045 - 0.090: 242 0.090 - 0.136: 58 0.136 - 0.181: 6 0.181 - 0.226: 1 Chirality restraints: 1151 Sorted by residual: chirality pdb=" CA ILE A 470 " pdb=" N ILE A 470 " pdb=" C ILE A 470 " pdb=" CB ILE A 470 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA THR D 449 " pdb=" N THR D 449 " pdb=" C THR D 449 " pdb=" CB THR D 449 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CA TYR A 485 " pdb=" N TYR A 485 " pdb=" C TYR A 485 " pdb=" CB TYR A 485 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 1148 not shown) Planarity restraints: 1131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 477 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" C ILE A 477 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE A 477 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A 478 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 474 " 0.035 5.00e-02 4.00e+02 5.22e-02 4.35e+00 pdb=" N PRO B 475 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 475 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 475 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 474 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO D 475 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 475 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 475 " 0.024 5.00e-02 4.00e+02 ... (remaining 1128 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 2147 2.81 - 3.39: 8112 3.39 - 3.98: 12618 3.98 - 4.56: 18663 4.56 - 5.14: 26936 Nonbonded interactions: 68476 Sorted by model distance: nonbonded pdb=" O THR C 388 " pdb=" OG SER C 392 " model vdw 2.229 3.040 nonbonded pdb=" O TYR D 323 " pdb=" OG1 THR D 326 " model vdw 2.253 3.040 nonbonded pdb=" O VAL A 407 " pdb=" OG SER A 411 " model vdw 2.266 3.040 nonbonded pdb=" OE2 GLU D 283 " pdb=" NH1 ARG D 368 " model vdw 2.305 3.120 nonbonded pdb=" NE2 HIS D 486 " pdb=" OH TYR G 10 " model vdw 2.332 3.120 ... (remaining 68471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 216 through 218 or (resid 219 and (name N or name CA or na \ me C or name O or name CB )) or resid 220 through 226 or (resid 227 and (name N \ or name CA or name C or name O or name CB )) or resid 228 through 489 or resid 7 \ 02 through 705)) selection = (chain 'B' and (resid 216 through 218 or (resid 219 and (name N or name CA or na \ me C or name O or name CB )) or resid 220 through 489 or resid 702 through 705)) \ selection = (chain 'C' and (resid 216 through 218 or (resid 219 and (name N or name CA or na \ me C or name O or name CB )) or resid 220 through 226 or (resid 227 and (name N \ or name CA or name C or name O or name CB )) or resid 228 through 489 or resid 7 \ 02 through 705)) selection = (chain 'D' and (resid 216 through 226 or (resid 227 and (name N or name CA or na \ me C or name O or name CB )) or resid 228 through 489 or resid 702 through 705)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.310 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 : 0.009 0.116 7184 Z= 0.465 Angle : 1.027 11.689 9649 Z= 0.459 Chirality : 0.045 0.226 1151 Planarity : 0.006 0.061 1131 Dihedral : 15.982 97.753 2563 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.27), residues: 821 helix: -0.92 (0.16), residues: 628 sheet: None (None), residues: 0 loop : 1.02 (0.59), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 387 TYR 0.019 0.001 TYR C 483 PHE 0.015 0.001 PHE B 217 TRP 0.010 0.002 TRP A 454 HIS 0.003 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00933 ( 7184) covalent geometry : angle 1.02673 ( 9649) hydrogen bonds : bond 0.12819 ( 501) hydrogen bonds : angle 4.73617 ( 1413) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.274 Fit side-chains REVERT: A 247 GLU cc_start: 0.8393 (tt0) cc_final: 0.8041 (tt0) REVERT: A 431 ASP cc_start: 0.8813 (t0) cc_final: 0.8391 (t0) REVERT: B 247 GLU cc_start: 0.8531 (tt0) cc_final: 0.8042 (pt0) REVERT: B 365 ARG cc_start: 0.8218 (mtp180) cc_final: 0.7958 (mmm160) REVERT: B 431 ASP cc_start: 0.9027 (t0) cc_final: 0.8665 (t0) REVERT: C 227 ARG cc_start: 0.7483 (ptt90) cc_final: 0.7242 (ptt90) REVERT: C 247 GLU cc_start: 0.8213 (pt0) cc_final: 0.7955 (pt0) REVERT: C 380 LYS cc_start: 0.8142 (mptt) cc_final: 0.7343 (mppt) REVERT: C 483 TYR cc_start: 0.8558 (t80) cc_final: 0.8335 (t80) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.7751 time to fit residues: 94.2810 Evaluate side-chains 98 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 480 ASN D 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.075478 restraints weight = 15808.093| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.03 r_work: 0.2872 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7184 Z= 0.138 Angle : 0.595 12.201 9649 Z= 0.307 Chirality : 0.041 0.182 1151 Planarity : 0.004 0.041 1131 Dihedral : 12.006 64.757 1133 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.66 % Allowed : 9.70 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.29), residues: 821 helix: 1.47 (0.19), residues: 636 sheet: None (None), residues: 0 loop : -0.12 (0.53), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 365 TYR 0.019 0.001 TYR B 323 PHE 0.010 0.001 PHE B 244 TRP 0.007 0.001 TRP C 454 HIS 0.003 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7184) covalent geometry : angle 0.59529 ( 9649) hydrogen bonds : bond 0.04633 ( 501) hydrogen bonds : angle 3.61231 ( 1413) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.267 Fit side-chains REVERT: A 247 GLU cc_start: 0.8836 (tt0) cc_final: 0.8481 (tt0) REVERT: A 431 ASP cc_start: 0.9269 (t0) cc_final: 0.8849 (m-30) REVERT: B 247 GLU cc_start: 0.8907 (tt0) cc_final: 0.8338 (pt0) REVERT: B 365 ARG cc_start: 0.7995 (mtp180) cc_final: 0.7769 (mmm160) REVERT: B 431 ASP cc_start: 0.9424 (t0) cc_final: 0.8978 (t0) REVERT: C 380 LYS cc_start: 0.7460 (mptt) cc_final: 0.7198 (mptt) REVERT: C 431 ASP cc_start: 0.9377 (OUTLIER) cc_final: 0.9117 (t70) REVERT: C 483 TYR cc_start: 0.8730 (t80) cc_final: 0.8475 (t80) REVERT: G 2 THR cc_start: 0.6629 (p) cc_final: 0.6345 (m) outliers start: 12 outliers final: 1 residues processed: 106 average time/residue: 0.7824 time to fit residues: 86.3191 Evaluate side-chains 100 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 403 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.097461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.075143 restraints weight = 15832.150| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.04 r_work: 0.2862 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7184 Z= 0.141 Angle : 0.575 11.005 9649 Z= 0.295 Chirality : 0.040 0.167 1151 Planarity : 0.004 0.042 1131 Dihedral : 10.566 59.754 1133 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.39 % Allowed : 12.47 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.30), residues: 821 helix: 2.29 (0.20), residues: 628 sheet: None (None), residues: 0 loop : -0.31 (0.51), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 387 TYR 0.017 0.001 TYR B 323 PHE 0.011 0.001 PHE B 244 TRP 0.005 0.001 TRP C 289 HIS 0.003 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7184) covalent geometry : angle 0.57516 ( 9649) hydrogen bonds : bond 0.04372 ( 501) hydrogen bonds : angle 3.44384 ( 1413) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 247 GLU cc_start: 0.8824 (tt0) cc_final: 0.8500 (tt0) REVERT: A 431 ASP cc_start: 0.9267 (t0) cc_final: 0.8901 (m-30) REVERT: B 247 GLU cc_start: 0.8905 (tt0) cc_final: 0.8363 (pt0) REVERT: B 431 ASP cc_start: 0.9419 (t0) cc_final: 0.8955 (t0) REVERT: C 380 LYS cc_start: 0.7588 (mptt) cc_final: 0.7302 (mptt) REVERT: C 395 GLU cc_start: 0.8256 (mp0) cc_final: 0.8030 (mp0) REVERT: C 431 ASP cc_start: 0.9370 (OUTLIER) cc_final: 0.9101 (t70) REVERT: C 483 TYR cc_start: 0.8725 (t80) cc_final: 0.8500 (t80) REVERT: G 2 THR cc_start: 0.6535 (p) cc_final: 0.6331 (m) outliers start: 10 outliers final: 2 residues processed: 112 average time/residue: 0.7848 time to fit residues: 91.4659 Evaluate side-chains 102 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 403 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 33 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.098781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.076521 restraints weight = 15947.231| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.06 r_work: 0.2887 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7184 Z= 0.126 Angle : 0.569 12.573 9649 Z= 0.288 Chirality : 0.040 0.179 1151 Planarity : 0.004 0.041 1131 Dihedral : 9.565 59.389 1133 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.66 % Allowed : 14.68 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.31), residues: 821 helix: 2.58 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -0.43 (0.51), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 387 TYR 0.023 0.001 TYR D 483 PHE 0.009 0.001 PHE B 244 TRP 0.004 0.001 TRP A 289 HIS 0.002 0.000 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7184) covalent geometry : angle 0.56866 ( 9649) hydrogen bonds : bond 0.04059 ( 501) hydrogen bonds : angle 3.27367 ( 1413) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.273 Fit side-chains REVERT: A 247 GLU cc_start: 0.8835 (tt0) cc_final: 0.8555 (tt0) REVERT: A 283 GLU cc_start: 0.8616 (tp30) cc_final: 0.8387 (mm-30) REVERT: A 431 ASP cc_start: 0.9246 (t0) cc_final: 0.8915 (m-30) REVERT: B 221 GLU cc_start: 0.8170 (mp0) cc_final: 0.7766 (mp0) REVERT: B 247 GLU cc_start: 0.8882 (tt0) cc_final: 0.8361 (pt0) REVERT: B 431 ASP cc_start: 0.9416 (t0) cc_final: 0.8896 (t0) REVERT: C 363 VAL cc_start: 0.8723 (p) cc_final: 0.8517 (p) REVERT: C 380 LYS cc_start: 0.7612 (mptt) cc_final: 0.7313 (mptt) REVERT: G 9 LEU cc_start: 0.7469 (mp) cc_final: 0.7235 (mt) outliers start: 12 outliers final: 6 residues processed: 118 average time/residue: 0.7983 time to fit residues: 97.9951 Evaluate side-chains 109 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 70 optimal weight: 0.0570 chunk 38 optimal weight: 3.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.075336 restraints weight = 15974.643| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.08 r_work: 0.2863 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.004 0.033 7184 Z= 0.157 Angle : 0.604 11.279 9649 Z= 0.306 Chirality : 0.041 0.184 1151 Planarity : 0.004 0.042 1131 Dihedral : 9.109 59.356 1133 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.22 % Allowed : 16.76 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.85 (0.31), residues: 821 helix: 2.56 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -0.60 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 365 TYR 0.011 0.001 TYR D 323 PHE 0.011 0.001 PHE B 244 TRP 0.005 0.001 TRP C 289 HIS 0.003 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 7184) covalent geometry : angle 0.60401 ( 9649) hydrogen bonds : bond 0.04277 ( 501) hydrogen bonds : angle 3.30569 ( 1413) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.282 Fit side-chains REVERT: A 247 GLU cc_start: 0.8852 (tt0) cc_final: 0.8574 (tt0) REVERT: A 380 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7533 (mppt) REVERT: A 431 ASP cc_start: 0.9266 (t0) cc_final: 0.8807 (m-30) REVERT: A 468 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8190 (mp) REVERT: B 221 GLU cc_start: 0.8183 (mp0) cc_final: 0.7794 (mp0) REVERT: B 247 GLU cc_start: 0.8927 (tt0) cc_final: 0.8408 (pt0) REVERT: B 431 ASP cc_start: 0.9427 (t0) cc_final: 0.8912 (t0) REVERT: C 380 LYS cc_start: 0.7680 (mptt) cc_final: 0.7350 (mptt) REVERT: C 395 GLU cc_start: 0.8358 (mp0) cc_final: 0.8105 (mp0) REVERT: C 431 ASP cc_start: 0.9344 (OUTLIER) cc_final: 0.9086 (t70) REVERT: D 380 LYS cc_start: 0.7836 (mptt) cc_final: 0.7543 (mppt) REVERT: G 9 LEU cc_start: 0.7554 (mp) cc_final: 0.7320 (mt) outliers start: 16 outliers final: 7 residues processed: 112 average time/residue: 0.7595 time to fit residues: 88.6570 Evaluate side-chains 109 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 79 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.098765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.076637 restraints weight = 15947.874| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.05 r_work: 0.2889 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7184 Z= 0.132 Angle : 0.597 10.564 9649 Z= 0.301 Chirality : 0.040 0.192 1151 Planarity : 0.004 0.042 1131 Dihedral : 8.551 58.399 1133 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.08 % Allowed : 17.73 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.99 (0.30), residues: 821 helix: 2.73 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -0.74 (0.49), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 387 TYR 0.022 0.001 TYR C 483 PHE 0.009 0.001 PHE B 244 TRP 0.005 0.001 TRP C 454 HIS 0.002 0.000 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7184) covalent geometry : angle 0.59729 ( 9649) hydrogen bonds : bond 0.04006 ( 501) hydrogen bonds : angle 3.20823 ( 1413) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.277 Fit side-chains REVERT: A 247 GLU cc_start: 0.8853 (tt0) cc_final: 0.8383 (pt0) REVERT: A 380 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7553 (mppt) REVERT: A 431 ASP cc_start: 0.9251 (t0) cc_final: 0.8859 (m-30) REVERT: A 468 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8217 (mp) REVERT: B 221 GLU cc_start: 0.8179 (mp0) cc_final: 0.7806 (mp0) REVERT: B 247 GLU cc_start: 0.8907 (tt0) cc_final: 0.8396 (pt0) REVERT: B 431 ASP cc_start: 0.9422 (t0) cc_final: 0.8892 (t0) REVERT: C 380 LYS cc_start: 0.7683 (mptt) cc_final: 0.7338 (mptt) REVERT: D 380 LYS cc_start: 0.7901 (mptt) cc_final: 0.7610 (mppt) REVERT: G 9 LEU cc_start: 0.7642 (mp) cc_final: 0.7409 (mt) outliers start: 15 outliers final: 7 residues processed: 119 average time/residue: 0.7434 time to fit residues: 92.2611 Evaluate side-chains 113 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.097863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.075570 restraints weight = 15784.273| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.03 r_work: 0.2870 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7184 Z= 0.154 Angle : 0.631 10.085 9649 Z= 0.317 Chirality : 0.040 0.213 1151 Planarity : 0.004 0.043 1131 Dihedral : 8.333 58.142 1133 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.35 % Allowed : 18.84 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.30), residues: 821 helix: 2.65 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -1.31 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 365 TYR 0.010 0.001 TYR D 323 PHE 0.011 0.001 PHE B 244 TRP 0.005 0.001 TRP C 289 HIS 0.002 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7184) covalent geometry : angle 0.63145 ( 9649) hydrogen bonds : bond 0.04182 ( 501) hydrogen bonds : angle 3.25870 ( 1413) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 247 GLU cc_start: 0.8873 (tt0) cc_final: 0.8608 (tt0) REVERT: A 380 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7555 (mppt) REVERT: A 431 ASP cc_start: 0.9270 (t0) cc_final: 0.8837 (m-30) REVERT: A 468 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8159 (mp) REVERT: B 221 GLU cc_start: 0.8174 (mp0) cc_final: 0.7820 (mp0) REVERT: B 247 GLU cc_start: 0.8928 (tt0) cc_final: 0.8427 (pt0) REVERT: B 431 ASP cc_start: 0.9417 (t0) cc_final: 0.8876 (t0) REVERT: C 380 LYS cc_start: 0.7760 (mptt) cc_final: 0.7413 (mptt) REVERT: C 431 ASP cc_start: 0.9356 (OUTLIER) cc_final: 0.9078 (t70) REVERT: D 380 LYS cc_start: 0.7916 (mptt) cc_final: 0.7618 (mppt) REVERT: D 468 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8057 (mp) REVERT: G 9 LEU cc_start: 0.7710 (mp) cc_final: 0.7379 (mt) outliers start: 17 outliers final: 7 residues processed: 116 average time/residue: 0.7147 time to fit residues: 86.5962 Evaluate side-chains 112 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain G residue 3 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 67 optimal weight: 4.9990 chunk 35 optimal weight: 0.0030 chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.098216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.075888 restraints weight = 15913.189| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.04 r_work: 0.2875 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7184 Z= 0.149 Angle : 0.638 9.848 9649 Z= 0.320 Chirality : 0.040 0.233 1151 Planarity : 0.004 0.043 1131 Dihedral : 8.133 57.366 1133 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.22 % Allowed : 19.11 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.06 (0.30), residues: 821 helix: 2.77 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -0.79 (0.49), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 387 TYR 0.024 0.001 TYR C 483 PHE 0.010 0.001 PHE B 244 TRP 0.005 0.001 TRP C 454 HIS 0.002 0.001 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 7184) covalent geometry : angle 0.63816 ( 9649) hydrogen bonds : bond 0.04144 ( 501) hydrogen bonds : angle 3.24205 ( 1413) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 247 GLU cc_start: 0.8873 (tt0) cc_final: 0.8605 (tt0) REVERT: A 380 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7550 (mppt) REVERT: A 431 ASP cc_start: 0.9275 (t0) cc_final: 0.8744 (t0) REVERT: A 468 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8199 (mp) REVERT: A 487 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8719 (ttp-170) REVERT: B 221 GLU cc_start: 0.8173 (mp0) cc_final: 0.7808 (mp0) REVERT: B 247 GLU cc_start: 0.8932 (tt0) cc_final: 0.8431 (pt0) REVERT: B 380 LYS cc_start: 0.8008 (pmtt) cc_final: 0.7582 (pmmt) REVERT: B 431 ASP cc_start: 0.9418 (t0) cc_final: 0.8853 (t0) REVERT: C 380 LYS cc_start: 0.7755 (mptt) cc_final: 0.7418 (mptt) REVERT: C 431 ASP cc_start: 0.9351 (OUTLIER) cc_final: 0.9083 (t70) REVERT: D 251 GLU cc_start: 0.8586 (mp0) cc_final: 0.8375 (mp0) REVERT: D 380 LYS cc_start: 0.7921 (mptt) cc_final: 0.7627 (mppt) REVERT: D 468 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8075 (mp) REVERT: G 9 LEU cc_start: 0.7671 (mp) cc_final: 0.7371 (mt) outliers start: 16 outliers final: 7 residues processed: 116 average time/residue: 0.7330 time to fit residues: 88.6589 Evaluate side-chains 114 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 468 LEU Chi-restraints excluded: chain G residue 3 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.101142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.078160 restraints weight = 16041.028| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.13 r_work: 0.2907 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7184 Z= 0.136 Angle : 0.637 9.791 9649 Z= 0.323 Chirality : 0.040 0.240 1151 Planarity : 0.004 0.042 1131 Dihedral : 7.845 59.363 1133 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.35 % Allowed : 18.84 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.13 (0.30), residues: 821 helix: 2.87 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -0.88 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 365 TYR 0.010 0.001 TYR D 323 PHE 0.009 0.001 PHE B 244 TRP 0.005 0.001 TRP A 454 HIS 0.002 0.000 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7184) covalent geometry : angle 0.63749 ( 9649) hydrogen bonds : bond 0.03953 ( 501) hydrogen bonds : angle 3.17420 ( 1413) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 247 GLU cc_start: 0.8811 (tt0) cc_final: 0.8534 (tt0) REVERT: A 380 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7474 (mppt) REVERT: A 431 ASP cc_start: 0.9282 (t0) cc_final: 0.8775 (t0) REVERT: A 468 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8154 (mp) REVERT: A 487 ARG cc_start: 0.9287 (OUTLIER) cc_final: 0.8723 (ttp-170) REVERT: B 221 GLU cc_start: 0.8092 (mp0) cc_final: 0.7746 (mp0) REVERT: B 247 GLU cc_start: 0.8869 (tt0) cc_final: 0.8365 (pt0) REVERT: B 380 LYS cc_start: 0.7974 (pmtt) cc_final: 0.7560 (pmmt) REVERT: B 431 ASP cc_start: 0.9411 (t0) cc_final: 0.8827 (t0) REVERT: C 380 LYS cc_start: 0.7659 (mptt) cc_final: 0.7344 (mptt) REVERT: C 395 GLU cc_start: 0.8379 (mp0) cc_final: 0.8100 (mp0) REVERT: C 427 LYS cc_start: 0.9318 (mmtt) cc_final: 0.9111 (mmpt) REVERT: C 431 ASP cc_start: 0.9316 (OUTLIER) cc_final: 0.9023 (t70) REVERT: D 251 GLU cc_start: 0.8595 (mp0) cc_final: 0.8371 (mp0) REVERT: D 380 LYS cc_start: 0.7871 (mptt) cc_final: 0.7579 (mppt) REVERT: D 468 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7949 (mp) outliers start: 17 outliers final: 8 residues processed: 117 average time/residue: 0.7252 time to fit residues: 88.5985 Evaluate side-chains 114 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.100383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.078256 restraints weight = 15816.749| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.02 r_work: 0.2931 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7184 Z= 0.131 Angle : 0.635 9.873 9649 Z= 0.321 Chirality : 0.040 0.243 1151 Planarity : 0.004 0.042 1131 Dihedral : 7.544 57.050 1133 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.08 % Allowed : 19.11 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.20 (0.30), residues: 821 helix: 2.93 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -0.90 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 387 TYR 0.027 0.002 TYR C 483 PHE 0.009 0.001 PHE B 244 TRP 0.005 0.001 TRP A 454 HIS 0.001 0.000 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7184) covalent geometry : angle 0.63465 ( 9649) hydrogen bonds : bond 0.03839 ( 501) hydrogen bonds : angle 3.14393 ( 1413) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 247 GLU cc_start: 0.8784 (tt0) cc_final: 0.8323 (pt0) REVERT: A 380 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7468 (mppt) REVERT: A 431 ASP cc_start: 0.9253 (t0) cc_final: 0.8784 (t0) REVERT: A 468 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8141 (mp) REVERT: A 487 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8716 (ttp-170) REVERT: B 221 GLU cc_start: 0.8098 (mp0) cc_final: 0.7771 (mp0) REVERT: B 247 GLU cc_start: 0.8872 (tt0) cc_final: 0.8369 (pt0) REVERT: B 380 LYS cc_start: 0.7968 (pmtt) cc_final: 0.7561 (pmmt) REVERT: B 431 ASP cc_start: 0.9396 (t0) cc_final: 0.8804 (t0) REVERT: C 380 LYS cc_start: 0.7619 (mptt) cc_final: 0.7324 (mptt) REVERT: C 395 GLU cc_start: 0.8338 (mp0) cc_final: 0.8069 (mp0) REVERT: C 431 ASP cc_start: 0.9306 (OUTLIER) cc_final: 0.9011 (t70) REVERT: D 251 GLU cc_start: 0.8574 (mp0) cc_final: 0.8338 (mp0) REVERT: D 380 LYS cc_start: 0.7835 (mptt) cc_final: 0.7554 (mppt) REVERT: D 468 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7921 (mp) outliers start: 15 outliers final: 9 residues processed: 117 average time/residue: 0.7555 time to fit residues: 92.1828 Evaluate side-chains 113 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 431 ASP Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 3 optimal weight: 0.2980 chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.100524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.078333 restraints weight = 15835.997| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.03 r_work: 0.2935 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7184 Z= 0.135 Angle : 0.657 10.806 9649 Z= 0.325 Chirality : 0.041 0.280 1151 Planarity : 0.004 0.043 1131 Dihedral : 7.355 58.390 1133 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.94 % Allowed : 19.67 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.20 (0.30), residues: 821 helix: 3.00 (0.20), residues: 628 sheet: None (None), residues: 0 loop : -1.09 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 297 TYR 0.025 0.001 TYR B 323 PHE 0.009 0.001 PHE B 244 TRP 0.004 0.001 TRP C 289 HIS 0.001 0.000 HIS A 486 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7184) covalent geometry : angle 0.65734 ( 9649) hydrogen bonds : bond 0.03822 ( 501) hydrogen bonds : angle 3.12729 ( 1413) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2472.68 seconds wall clock time: 42 minutes 59.30 seconds (2579.30 seconds total)