Starting phenix.real_space_refine on Sat Aug 23 22:35:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vxm_21444/08_2025/6vxm_21444.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxm_21444/08_2025/6vxm_21444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vxm_21444/08_2025/6vxm_21444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxm_21444/08_2025/6vxm_21444.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vxm_21444/08_2025/6vxm_21444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxm_21444/08_2025/6vxm_21444.map" } resolution = 3.06 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 9779 2.51 5 N 2485 2.21 5 O 2716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15064 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "B" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "C" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "D" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "E" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "F" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "G" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2117 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 8, 'TRANS': 268} Chain breaks: 2 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'LFA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'LFA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'LFA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'LFA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'LFA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'LFA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'LFA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Time building chain proxies: 2.91, per 1000 atoms: 0.19 Number of scatterers: 15064 At special positions: 0 Unit cell: (102.3, 102.3, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 2716 8.00 N 2485 7.00 C 9779 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: 0.84 Conformation dependent library (CDL) restraints added in 447.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3598 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 8 sheets defined 58.5% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 204 through 228 Proline residue: A 212 - end of helix removed outlier: 3.589A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 266 Processing helix chain 'A' and resid 277 through 304 Processing helix chain 'A' and resid 306 through 325 Processing helix chain 'A' and resid 325 through 341 Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 463 through 484 removed outlier: 3.553A pdb=" N TYR A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 228 Proline residue: B 212 - end of helix removed outlier: 3.588A pdb=" N ILE B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 266 Processing helix chain 'B' and resid 277 through 304 Processing helix chain 'B' and resid 306 through 325 Processing helix chain 'B' and resid 325 through 341 Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 413 through 427 Processing helix chain 'B' and resid 463 through 484 removed outlier: 3.552A pdb=" N TYR B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 228 Proline residue: C 212 - end of helix removed outlier: 3.588A pdb=" N ILE C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 266 Processing helix chain 'C' and resid 277 through 304 Processing helix chain 'C' and resid 306 through 325 Processing helix chain 'C' and resid 325 through 341 Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 410 through 412 No H-bonds generated for 'chain 'C' and resid 410 through 412' Processing helix chain 'C' and resid 413 through 427 Processing helix chain 'C' and resid 463 through 484 removed outlier: 3.554A pdb=" N TYR C 467 " --> pdb=" O LYS C 463 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS C 484 " --> pdb=" O ILE C 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 228 Proline residue: D 212 - end of helix removed outlier: 3.588A pdb=" N ILE D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 266 Processing helix chain 'D' and resid 277 through 304 Processing helix chain 'D' and resid 306 through 325 Processing helix chain 'D' and resid 325 through 341 Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 413 through 427 Processing helix chain 'D' and resid 463 through 484 removed outlier: 3.552A pdb=" N TYR D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS D 484 " --> pdb=" O ILE D 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 228 Proline residue: E 212 - end of helix removed outlier: 3.588A pdb=" N ILE E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 266 Processing helix chain 'E' and resid 277 through 304 Processing helix chain 'E' and resid 306 through 325 Processing helix chain 'E' and resid 325 through 341 Processing helix chain 'E' and resid 382 through 384 No H-bonds generated for 'chain 'E' and resid 382 through 384' Processing helix chain 'E' and resid 410 through 412 No H-bonds generated for 'chain 'E' and resid 410 through 412' Processing helix chain 'E' and resid 413 through 427 Processing helix chain 'E' and resid 463 through 484 removed outlier: 3.553A pdb=" N TYR E 467 " --> pdb=" O LYS E 463 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS E 484 " --> pdb=" O ILE E 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 228 Proline residue: F 212 - end of helix removed outlier: 3.588A pdb=" N ILE F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 266 Processing helix chain 'F' and resid 277 through 304 Processing helix chain 'F' and resid 306 through 325 Processing helix chain 'F' and resid 325 through 341 Processing helix chain 'F' and resid 382 through 384 No H-bonds generated for 'chain 'F' and resid 382 through 384' Processing helix chain 'F' and resid 410 through 412 No H-bonds generated for 'chain 'F' and resid 410 through 412' Processing helix chain 'F' and resid 413 through 427 Processing helix chain 'F' and resid 463 through 484 removed outlier: 3.553A pdb=" N TYR F 467 " --> pdb=" O LYS F 463 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N HIS F 484 " --> pdb=" O ILE F 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 228 Proline residue: G 212 - end of helix removed outlier: 3.588A pdb=" N ILE G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 266 Processing helix chain 'G' and resid 277 through 304 Processing helix chain 'G' and resid 306 through 325 Processing helix chain 'G' and resid 325 through 341 Processing helix chain 'G' and resid 382 through 384 No H-bonds generated for 'chain 'G' and resid 382 through 384' Processing helix chain 'G' and resid 410 through 412 No H-bonds generated for 'chain 'G' and resid 410 through 412' Processing helix chain 'G' and resid 413 through 427 Processing helix chain 'G' and resid 463 through 484 removed outlier: 3.552A pdb=" N TYR G 467 " --> pdb=" O LYS G 463 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS G 484 " --> pdb=" O ILE G 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 352 removed outlier: 5.934A pdb=" N VAL A 359 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU A 370 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL G 359 " --> pdb=" O LEU G 370 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU G 370 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL F 359 " --> pdb=" O LEU F 370 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU F 370 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL E 359 " --> pdb=" O LEU E 370 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU E 370 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL D 359 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU D 370 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL C 359 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU C 370 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL B 359 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 370 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 439 through 446 removed outlier: 6.764A pdb=" N GLU A 451 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL A 445 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 487 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 439 through 446 removed outlier: 6.764A pdb=" N GLU B 451 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL B 445 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B 487 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 439 through 446 removed outlier: 6.764A pdb=" N GLU C 451 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL C 445 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER C 487 " --> pdb=" O GLN C 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 439 through 446 removed outlier: 6.764A pdb=" N GLU D 451 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL D 445 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE D 449 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER D 487 " --> pdb=" O GLN D 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 439 through 446 removed outlier: 6.764A pdb=" N GLU E 451 " --> pdb=" O SER E 443 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL E 445 " --> pdb=" O PHE E 449 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE E 449 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER E 487 " --> pdb=" O GLN E 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 439 through 446 removed outlier: 6.764A pdb=" N GLU F 451 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL F 445 " --> pdb=" O PHE F 449 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE F 449 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER F 487 " --> pdb=" O GLN F 407 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 439 through 446 removed outlier: 6.764A pdb=" N GLU G 451 " --> pdb=" O SER G 443 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL G 445 " --> pdb=" O PHE G 449 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE G 449 " --> pdb=" O VAL G 445 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER G 487 " --> pdb=" O GLN G 407 " (cutoff:3.500A) 1071 hydrogen bonds defined for protein. 3150 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: 2.18 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4300 1.33 - 1.45: 2268 1.45 - 1.57: 8559 1.57 - 1.69: 0 1.69 - 1.80: 147 Bond restraints: 15274 Sorted by residual: bond pdb=" C11 LFA E1102 " pdb=" C12 LFA E1102 " ideal model delta sigma weight residual 1.524 1.383 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C11 LFA B1101 " pdb=" C12 LFA B1101 " ideal model delta sigma weight residual 1.524 1.383 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C7 LFA D1101 " pdb=" C8 LFA D1101 " ideal model delta sigma weight residual 1.524 1.383 0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C7 LFA A1101 " pdb=" C8 LFA A1101 " ideal model delta sigma weight residual 1.524 1.383 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C8 LFA G1103 " pdb=" C9 LFA G1103 " ideal model delta sigma weight residual 1.524 1.384 0.140 2.00e-02 2.50e+03 4.93e+01 ... (remaining 15269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 20070 2.51 - 5.01: 208 5.01 - 7.52: 239 7.52 - 10.03: 4 10.03 - 12.53: 17 Bond angle restraints: 20538 Sorted by residual: angle pdb=" N THR C 264 " pdb=" CA THR C 264 " pdb=" C THR C 264 " ideal model delta sigma weight residual 113.12 100.59 12.53 1.25e+00 6.40e-01 1.01e+02 angle pdb=" N THR G 264 " pdb=" CA THR G 264 " pdb=" C THR G 264 " ideal model delta sigma weight residual 113.12 100.59 12.53 1.25e+00 6.40e-01 1.00e+02 angle pdb=" N THR F 264 " pdb=" CA THR F 264 " pdb=" C THR F 264 " ideal model delta sigma weight residual 113.12 100.61 12.51 1.25e+00 6.40e-01 1.00e+02 angle pdb=" N THR E 264 " pdb=" CA THR E 264 " pdb=" C THR E 264 " ideal model delta sigma weight residual 113.12 100.61 12.51 1.25e+00 6.40e-01 1.00e+02 angle pdb=" N THR D 264 " pdb=" CA THR D 264 " pdb=" C THR D 264 " ideal model delta sigma weight residual 113.12 100.62 12.50 1.25e+00 6.40e-01 1.00e+02 ... (remaining 20533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.62: 8303 13.62 - 27.24: 637 27.24 - 40.86: 237 40.86 - 54.48: 42 54.48 - 68.10: 35 Dihedral angle restraints: 9254 sinusoidal: 3703 harmonic: 5551 Sorted by residual: dihedral pdb=" CA ASN G 261 " pdb=" CB ASN G 261 " pdb=" CG ASN G 261 " pdb=" OD1 ASN G 261 " ideal model delta sinusoidal sigma weight residual 120.00 -171.90 -68.10 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASN F 261 " pdb=" CB ASN F 261 " pdb=" CG ASN F 261 " pdb=" OD1 ASN F 261 " ideal model delta sinusoidal sigma weight residual 120.00 -171.90 -68.10 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASN D 261 " pdb=" CB ASN D 261 " pdb=" CG ASN D 261 " pdb=" OD1 ASN D 261 " ideal model delta sinusoidal sigma weight residual 120.00 -171.91 -68.09 2 2.00e+01 2.50e-03 1.03e+01 ... (remaining 9251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1791 0.051 - 0.103: 533 0.103 - 0.154: 102 0.154 - 0.206: 3 0.206 - 0.257: 14 Chirality restraints: 2443 Sorted by residual: chirality pdb=" CA MET C 266 " pdb=" N MET C 266 " pdb=" C MET C 266 " pdb=" CB MET C 266 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA MET B 266 " pdb=" N MET B 266 " pdb=" C MET B 266 " pdb=" CB MET B 266 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA MET G 266 " pdb=" N MET G 266 " pdb=" C MET G 266 " pdb=" CB MET G 266 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 2440 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 375 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO B 376 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 376 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 376 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 375 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO C 376 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 376 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 376 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 375 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO E 376 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO E 376 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 376 " 0.026 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1940 2.75 - 3.29: 14014 3.29 - 3.82: 23257 3.82 - 4.36: 27755 4.36 - 4.90: 50396 Nonbonded interactions: 117362 Sorted by model distance: nonbonded pdb=" OG SER G 443 " pdb=" OE1 GLU G 451 " model vdw 2.208 3.040 nonbonded pdb=" OG SER B 443 " pdb=" OE1 GLU B 451 " model vdw 2.209 3.040 nonbonded pdb=" OG SER F 443 " pdb=" OE1 GLU F 451 " model vdw 2.209 3.040 nonbonded pdb=" OG SER E 443 " pdb=" OE1 GLU E 451 " model vdw 2.209 3.040 nonbonded pdb=" OG SER A 443 " pdb=" OE1 GLU A 451 " model vdw 2.209 3.040 ... (remaining 117357 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.600 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.018 0.141 15274 Z= 0.885 Angle : 1.016 12.532 20538 Z= 0.522 Chirality : 0.052 0.257 2443 Planarity : 0.005 0.047 2520 Dihedral : 12.836 68.101 5656 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % 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: -2.02 (0.17), residues: 1897 helix: -0.02 (0.15), residues: 1092 sheet: -2.53 (0.24), residues: 280 loop : -3.35 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 444 TYR 0.011 0.002 TYR E 441 PHE 0.010 0.002 PHE C 340 TRP 0.005 0.001 TRP E 397 HIS 0.005 0.002 HIS E 439 Details of bonding type rmsd covalent geometry : bond 0.01799 (15274) covalent geometry : angle 1.01628 (20538) hydrogen bonds : bond 0.12978 ( 1071) hydrogen bonds : angle 5.85918 ( 3150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.544 Fit side-chains REVERT: B 215 TYR cc_start: 0.7145 (m-80) cc_final: 0.6755 (m-80) REVERT: C 215 TYR cc_start: 0.7050 (m-80) cc_final: 0.6739 (m-80) REVERT: C 410 ASP cc_start: 0.7046 (t0) cc_final: 0.6603 (t0) REVERT: D 410 ASP cc_start: 0.7084 (t0) cc_final: 0.6881 (t0) REVERT: E 410 ASP cc_start: 0.7095 (t0) cc_final: 0.6632 (t0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.0839 time to fit residues: 24.0128 Evaluate side-chains 125 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN A 331 ASN A 339 GLN A 387 GLN A 428 ASN B 308 GLN B 331 ASN B 339 GLN B 387 GLN C 308 GLN C 331 ASN C 339 GLN C 387 GLN C 428 ASN D 261 ASN D 308 GLN D 331 ASN D 339 GLN D 387 GLN E 308 GLN E 331 ASN E 339 GLN E 387 GLN E 428 ASN F 308 GLN F 331 ASN F 339 GLN F 387 GLN G 308 GLN G 331 ASN G 339 GLN G 387 GLN G 428 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.090013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.065733 restraints weight = 32089.183| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.25 r_work: 0.2729 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.003 0.040 15274 Z= 0.124 Angle : 0.490 7.212 20538 Z= 0.247 Chirality : 0.039 0.150 2443 Planarity : 0.004 0.037 2520 Dihedral : 7.680 54.638 2212 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.24 % Allowed : 9.09 % Favored : 89.67 % 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: -0.12 (0.20), residues: 1897 helix: 1.67 (0.16), residues: 1141 sheet: -2.33 (0.26), residues: 273 loop : -3.05 (0.20), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 265 TYR 0.007 0.001 TYR D 238 PHE 0.005 0.001 PHE B 323 TRP 0.013 0.001 TRP C 253 HIS 0.001 0.000 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00270 (15274) covalent geometry : angle 0.48966 (20538) hydrogen bonds : bond 0.03843 ( 1071) hydrogen bonds : angle 3.89870 ( 3150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 410 ASP cc_start: 0.8950 (t0) cc_final: 0.8577 (t0) REVERT: D 346 MET cc_start: 0.9319 (tpp) cc_final: 0.9054 (mmm) REVERT: D 410 ASP cc_start: 0.8808 (t0) cc_final: 0.8372 (t0) REVERT: E 410 ASP cc_start: 0.8995 (t0) cc_final: 0.8634 (t0) REVERT: F 410 ASP cc_start: 0.8863 (t0) cc_final: 0.8327 (t0) outliers start: 20 outliers final: 11 residues processed: 142 average time/residue: 0.0736 time to fit residues: 17.4494 Evaluate side-chains 132 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 23 optimal weight: 5.9990 chunk 156 optimal weight: 0.1980 chunk 172 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 428 ASN D 428 ASN F 428 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.086187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.062132 restraints weight = 32856.217| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.25 r_work: 0.2656 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 15274 Z= 0.222 Angle : 0.530 7.405 20538 Z= 0.267 Chirality : 0.041 0.156 2443 Planarity : 0.004 0.038 2520 Dihedral : 6.755 51.295 2212 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.47 % Allowed : 9.77 % Favored : 87.76 % 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: 0.87 (0.20), residues: 1897 helix: 2.41 (0.16), residues: 1141 sheet: -1.78 (0.27), residues: 273 loop : -2.62 (0.22), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 460 TYR 0.007 0.001 TYR D 441 PHE 0.012 0.001 PHE A 323 TRP 0.010 0.001 TRP C 253 HIS 0.002 0.001 HIS G 484 Details of bonding type rmsd covalent geometry : bond 0.00530 (15274) covalent geometry : angle 0.53049 (20538) hydrogen bonds : bond 0.04295 ( 1071) hydrogen bonds : angle 3.80223 ( 3150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6742 (OUTLIER) cc_final: 0.6338 (m-80) REVERT: B 215 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.6508 (m-80) REVERT: C 410 ASP cc_start: 0.8935 (t0) cc_final: 0.8444 (t0) REVERT: D 215 TYR cc_start: 0.6964 (OUTLIER) cc_final: 0.6371 (m-80) REVERT: D 410 ASP cc_start: 0.8778 (t0) cc_final: 0.8350 (t0) REVERT: D 424 MET cc_start: 0.9027 (tmm) cc_final: 0.8732 (tmm) REVERT: E 215 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.6420 (m-80) REVERT: E 410 ASP cc_start: 0.8945 (t0) cc_final: 0.8489 (t0) REVERT: F 215 TYR cc_start: 0.6897 (OUTLIER) cc_final: 0.6190 (m-80) outliers start: 40 outliers final: 30 residues processed: 139 average time/residue: 0.0692 time to fit residues: 16.3622 Evaluate side-chains 157 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 413 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 76 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.089300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.065257 restraints weight = 32189.864| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.23 r_work: 0.2717 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15274 Z= 0.102 Angle : 0.427 7.260 20538 Z= 0.211 Chirality : 0.039 0.137 2443 Planarity : 0.003 0.032 2520 Dihedral : 6.193 58.551 2212 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.30 % Allowed : 11.81 % Favored : 86.89 % 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: 1.66 (0.20), residues: 1897 helix: 3.07 (0.16), residues: 1099 sheet: -1.28 (0.29), residues: 280 loop : -2.06 (0.22), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 460 TYR 0.005 0.001 TYR F 467 PHE 0.005 0.001 PHE F 323 TRP 0.011 0.001 TRP C 253 HIS 0.001 0.000 HIS E 484 Details of bonding type rmsd covalent geometry : bond 0.00218 (15274) covalent geometry : angle 0.42713 (20538) hydrogen bonds : bond 0.03330 ( 1071) hydrogen bonds : angle 3.48265 ( 3150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6673 (OUTLIER) cc_final: 0.6279 (m-80) REVERT: B 215 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.6430 (m-80) REVERT: C 348 ASP cc_start: 0.9068 (m-30) cc_final: 0.8713 (m-30) REVERT: C 410 ASP cc_start: 0.8930 (t0) cc_final: 0.8468 (t0) REVERT: C 424 MET cc_start: 0.9145 (tmm) cc_final: 0.8941 (tmm) REVERT: D 215 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6404 (m-80) REVERT: D 348 ASP cc_start: 0.8972 (m-30) cc_final: 0.8594 (m-30) REVERT: D 410 ASP cc_start: 0.8754 (t0) cc_final: 0.8335 (t0) REVERT: E 215 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.6429 (m-80) REVERT: E 410 ASP cc_start: 0.8908 (t0) cc_final: 0.8436 (t0) REVERT: F 215 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.6118 (m-80) outliers start: 21 outliers final: 15 residues processed: 144 average time/residue: 0.0709 time to fit residues: 17.6731 Evaluate side-chains 152 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 15 optimal weight: 0.3980 chunk 29 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.087530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.063608 restraints weight = 32688.578| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.24 r_work: 0.2686 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15274 Z= 0.155 Angle : 0.453 7.001 20538 Z= 0.226 Chirality : 0.039 0.127 2443 Planarity : 0.003 0.031 2520 Dihedral : 6.171 58.908 2212 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.72 % Allowed : 11.56 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.97 (0.20), residues: 1897 helix: 3.25 (0.16), residues: 1099 sheet: -0.85 (0.30), residues: 280 loop : -1.94 (0.23), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 460 TYR 0.004 0.001 TYR A 441 PHE 0.009 0.001 PHE A 323 TRP 0.007 0.001 TRP C 253 HIS 0.001 0.000 HIS G 484 Details of bonding type rmsd covalent geometry : bond 0.00361 (15274) covalent geometry : angle 0.45318 (20538) hydrogen bonds : bond 0.03611 ( 1071) hydrogen bonds : angle 3.50954 ( 3150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 133 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6706 (OUTLIER) cc_final: 0.6350 (m-80) REVERT: B 215 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.6475 (m-80) REVERT: B 267 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8527 (tt) REVERT: C 348 ASP cc_start: 0.9087 (m-30) cc_final: 0.8739 (m-30) REVERT: C 410 ASP cc_start: 0.8928 (t0) cc_final: 0.8475 (t0) REVERT: D 215 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.6436 (m-80) REVERT: D 348 ASP cc_start: 0.8988 (m-30) cc_final: 0.8616 (m-30) REVERT: D 410 ASP cc_start: 0.8726 (t0) cc_final: 0.8220 (t0) REVERT: E 215 TYR cc_start: 0.6779 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: E 410 ASP cc_start: 0.8902 (t0) cc_final: 0.8441 (t0) REVERT: F 215 TYR cc_start: 0.6893 (OUTLIER) cc_final: 0.6187 (m-80) REVERT: G 249 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8372 (mm) REVERT: G 267 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8512 (tt) outliers start: 44 outliers final: 31 residues processed: 156 average time/residue: 0.0704 time to fit residues: 18.6769 Evaluate side-chains 172 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 187 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.087922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.064064 restraints weight = 32542.104| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.22 r_work: 0.2698 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15274 Z= 0.133 Angle : 0.441 7.497 20538 Z= 0.216 Chirality : 0.039 0.127 2443 Planarity : 0.003 0.030 2520 Dihedral : 6.027 59.149 2212 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.10 % Allowed : 12.49 % Favored : 85.41 % 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: 2.16 (0.20), residues: 1897 helix: 3.37 (0.15), residues: 1099 sheet: -0.75 (0.31), residues: 287 loop : -1.82 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 426 TYR 0.004 0.001 TYR C 441 PHE 0.007 0.001 PHE D 323 TRP 0.007 0.001 TRP C 253 HIS 0.001 0.000 HIS G 484 Details of bonding type rmsd covalent geometry : bond 0.00304 (15274) covalent geometry : angle 0.44051 (20538) hydrogen bonds : bond 0.03386 ( 1071) hydrogen bonds : angle 3.42802 ( 3150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6757 (OUTLIER) cc_final: 0.6391 (m-80) REVERT: B 215 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.6509 (m-80) REVERT: B 267 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8600 (tt) REVERT: C 348 ASP cc_start: 0.9088 (m-30) cc_final: 0.8881 (m-30) REVERT: C 410 ASP cc_start: 0.8924 (t0) cc_final: 0.8468 (t0) REVERT: D 215 TYR cc_start: 0.7040 (OUTLIER) cc_final: 0.6470 (m-80) REVERT: D 348 ASP cc_start: 0.8979 (m-30) cc_final: 0.8601 (m-30) REVERT: D 410 ASP cc_start: 0.8692 (t0) cc_final: 0.8196 (t0) REVERT: E 215 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.6404 (m-80) REVERT: E 410 ASP cc_start: 0.8855 (t0) cc_final: 0.8446 (t0) REVERT: F 215 TYR cc_start: 0.6960 (OUTLIER) cc_final: 0.6180 (m-80) REVERT: G 249 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8383 (mm) outliers start: 34 outliers final: 26 residues processed: 150 average time/residue: 0.0676 time to fit residues: 17.2280 Evaluate side-chains 165 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 183 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 162 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.085022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.061430 restraints weight = 32717.537| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.22 r_work: 0.2650 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 15274 Z= 0.243 Angle : 0.525 7.983 20538 Z= 0.260 Chirality : 0.041 0.133 2443 Planarity : 0.003 0.034 2520 Dihedral : 6.377 58.269 2212 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.66 % Allowed : 12.18 % Favored : 85.16 % 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: 1.90 (0.21), residues: 1897 helix: 3.07 (0.16), residues: 1141 sheet: -0.73 (0.31), residues: 280 loop : -2.23 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 426 TYR 0.005 0.001 TYR G 256 PHE 0.012 0.001 PHE A 323 TRP 0.005 0.001 TRP C 253 HIS 0.001 0.001 HIS G 484 Details of bonding type rmsd covalent geometry : bond 0.00577 (15274) covalent geometry : angle 0.52468 (20538) hydrogen bonds : bond 0.04015 ( 1071) hydrogen bonds : angle 3.65651 ( 3150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.6439 (m-80) REVERT: A 311 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8627 (mp) REVERT: B 215 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.6521 (m-80) REVERT: B 267 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8625 (tt) REVERT: C 348 ASP cc_start: 0.9109 (m-30) cc_final: 0.8775 (m-30) REVERT: C 410 ASP cc_start: 0.8917 (t0) cc_final: 0.8495 (t0) REVERT: D 215 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.6514 (m-80) REVERT: D 410 ASP cc_start: 0.8689 (t0) cc_final: 0.8199 (t0) REVERT: E 215 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.6450 (m-80) REVERT: E 410 ASP cc_start: 0.8850 (t0) cc_final: 0.8494 (t0) REVERT: F 215 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6208 (m-80) REVERT: G 249 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8466 (mm) outliers start: 43 outliers final: 32 residues processed: 152 average time/residue: 0.0654 time to fit residues: 17.1724 Evaluate side-chains 169 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 284 ASP Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 413 MET Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 33 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 110 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.088283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.064611 restraints weight = 32358.958| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.23 r_work: 0.2707 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15274 Z= 0.101 Angle : 0.426 8.230 20538 Z= 0.208 Chirality : 0.038 0.123 2443 Planarity : 0.003 0.030 2520 Dihedral : 5.985 59.310 2212 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.18 % Allowed : 13.61 % Favored : 85.22 % 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: 2.40 (0.20), residues: 1897 helix: 3.52 (0.15), residues: 1099 sheet: -0.48 (0.32), residues: 287 loop : -1.73 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 326 TYR 0.003 0.000 TYR G 238 PHE 0.006 0.001 PHE D 323 TRP 0.008 0.001 TRP C 253 HIS 0.001 0.000 HIS F 439 Details of bonding type rmsd covalent geometry : bond 0.00217 (15274) covalent geometry : angle 0.42637 (20538) hydrogen bonds : bond 0.03217 ( 1071) hydrogen bonds : angle 3.37820 ( 3150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6742 (OUTLIER) cc_final: 0.6384 (m-80) REVERT: B 215 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.6464 (m-80) REVERT: C 410 ASP cc_start: 0.8926 (t0) cc_final: 0.8495 (t0) REVERT: D 215 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.6491 (m-80) REVERT: D 348 ASP cc_start: 0.8969 (m-30) cc_final: 0.8585 (m-30) REVERT: D 410 ASP cc_start: 0.8661 (t0) cc_final: 0.8331 (t0) REVERT: E 215 TYR cc_start: 0.6807 (OUTLIER) cc_final: 0.6346 (m-80) REVERT: E 410 ASP cc_start: 0.8832 (t0) cc_final: 0.8469 (t0) REVERT: F 215 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.6137 (m-80) REVERT: G 249 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8326 (mm) outliers start: 19 outliers final: 13 residues processed: 148 average time/residue: 0.0736 time to fit residues: 18.4690 Evaluate side-chains 153 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 65 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.087880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.064109 restraints weight = 32364.397| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 3.23 r_work: 0.2693 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15274 Z= 0.130 Angle : 0.439 7.634 20538 Z= 0.215 Chirality : 0.039 0.129 2443 Planarity : 0.003 0.030 2520 Dihedral : 6.015 59.897 2212 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.36 % Allowed : 13.48 % Favored : 85.16 % 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: 2.50 (0.20), residues: 1897 helix: 3.58 (0.15), residues: 1099 sheet: -0.37 (0.33), residues: 287 loop : -1.68 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 426 TYR 0.003 0.001 TYR C 441 PHE 0.008 0.001 PHE A 323 TRP 0.006 0.001 TRP C 253 HIS 0.001 0.000 HIS E 484 Details of bonding type rmsd covalent geometry : bond 0.00298 (15274) covalent geometry : angle 0.43867 (20538) hydrogen bonds : bond 0.03345 ( 1071) hydrogen bonds : angle 3.39408 ( 3150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6747 (OUTLIER) cc_final: 0.6437 (m-80) REVERT: B 215 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.6463 (m-80) REVERT: B 267 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8652 (tt) REVERT: C 410 ASP cc_start: 0.8933 (t0) cc_final: 0.8530 (t0) REVERT: D 215 TYR cc_start: 0.7040 (OUTLIER) cc_final: 0.6534 (m-80) REVERT: D 348 ASP cc_start: 0.8984 (m-30) cc_final: 0.8598 (m-30) REVERT: D 410 ASP cc_start: 0.8652 (t0) cc_final: 0.8334 (t0) REVERT: E 215 TYR cc_start: 0.6809 (OUTLIER) cc_final: 0.6346 (m-80) REVERT: E 410 ASP cc_start: 0.8827 (t0) cc_final: 0.8488 (t0) REVERT: F 215 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.6112 (m-80) REVERT: F 249 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8298 (mm) REVERT: G 249 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8354 (mm) outliers start: 22 outliers final: 14 residues processed: 149 average time/residue: 0.0660 time to fit residues: 16.9112 Evaluate side-chains 157 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 75 optimal weight: 4.9990 chunk 160 optimal weight: 0.9990 chunk 105 optimal weight: 0.0870 chunk 171 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 128 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.089058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.065292 restraints weight = 32407.079| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.24 r_work: 0.2721 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15274 Z= 0.096 Angle : 0.413 7.360 20538 Z= 0.201 Chirality : 0.038 0.125 2443 Planarity : 0.003 0.029 2520 Dihedral : 5.748 56.098 2212 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.18 % Allowed : 13.79 % Favored : 85.03 % 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: 2.61 (0.20), residues: 1897 helix: 3.66 (0.15), residues: 1099 sheet: -0.31 (0.33), residues: 287 loop : -1.62 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 326 TYR 0.002 0.000 TYR C 441 PHE 0.005 0.001 PHE A 323 TRP 0.007 0.001 TRP C 253 HIS 0.001 0.000 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00205 (15274) covalent geometry : angle 0.41277 (20538) hydrogen bonds : bond 0.03038 ( 1071) hydrogen bonds : angle 3.26347 ( 3150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3794 Ramachandran restraints generated. 1897 Oldfield, 0 Emsley, 1897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6776 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: B 215 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.6449 (m-80) REVERT: B 267 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8660 (tt) REVERT: C 410 ASP cc_start: 0.8908 (t0) cc_final: 0.8511 (t0) REVERT: D 215 TYR cc_start: 0.6990 (OUTLIER) cc_final: 0.6505 (m-80) REVERT: D 348 ASP cc_start: 0.8905 (m-30) cc_final: 0.8522 (m-30) REVERT: D 410 ASP cc_start: 0.8666 (t0) cc_final: 0.8356 (t0) REVERT: E 215 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.6367 (m-80) REVERT: E 410 ASP cc_start: 0.8830 (t0) cc_final: 0.8496 (t0) REVERT: F 215 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.6119 (m-80) REVERT: G 249 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8293 (mm) REVERT: G 348 ASP cc_start: 0.8880 (m-30) cc_final: 0.8481 (m-30) outliers start: 19 outliers final: 12 residues processed: 151 average time/residue: 0.0654 time to fit residues: 17.0802 Evaluate side-chains 156 residues out of total 1617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 215 TYR Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain F residue 215 TYR Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 249 LEU Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 445 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 28 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 19 optimal weight: 0.0470 chunk 118 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.088851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.065171 restraints weight = 32341.235| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.24 r_work: 0.2721 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15274 Z= 0.097 Angle : 0.411 7.293 20538 Z= 0.201 Chirality : 0.038 0.126 2443 Planarity : 0.003 0.026 2520 Dihedral : 5.642 58.544 2212 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.42 % Allowed : 13.30 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.70 (0.20), residues: 1897 helix: 3.72 (0.15), residues: 1099 sheet: -0.24 (0.34), residues: 287 loop : -1.57 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 444 TYR 0.003 0.000 TYR B 441 PHE 0.005 0.001 PHE A 323 TRP 0.006 0.001 TRP C 253 HIS 0.001 0.000 HIS F 439 Details of bonding type rmsd covalent geometry : bond 0.00209 (15274) covalent geometry : angle 0.41121 (20538) hydrogen bonds : bond 0.03020 ( 1071) hydrogen bonds : angle 3.24157 ( 3150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2348.63 seconds wall clock time: 41 minutes 10.23 seconds (2470.23 seconds total)