Starting phenix.real_space_refine on Fri Sep 27 05:43:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/09_2024/6vxm_21444.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/09_2024/6vxm_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/09_2024/6vxm_21444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/09_2024/6vxm_21444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/09_2024/6vxm_21444.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxm_21444/09_2024/6vxm_21444.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 8.48, per 1000 atoms: 0.56 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: 3.49 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.62 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: 4.57 Time building geometry restraints manager: 4.02 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: 0.00 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 33.010 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.210 ------------------------------------------------------------------------------- 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= 1.180 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.001 TRP E 397 HIS 0.005 0.002 HIS E 439 PHE 0.010 0.002 PHE C 340 TYR 0.011 0.002 TYR E 441 ARG 0.004 0.001 ARG C 444 *********************** 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 fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.692 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: 0.2196 time to fit residues: 61.8428 Evaluate side-chains 125 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 171 optimal weight: 0.0270 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 308 GLN A 331 ASN A 339 GLN A 387 GLN A 428 ASN B 261 ASN B 308 GLN B 331 ASN B 339 GLN B 387 GLN B 428 ASN 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 D 428 ASN E 308 GLN E 331 ASN E 339 GLN E 387 GLN E 428 ASN F 261 ASN F 308 GLN F 331 ASN F 339 GLN F 387 GLN F 428 ASN G 261 ASN G 308 GLN G 331 ASN G 339 GLN G 387 GLN G 428 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15274 Z= 0.146 Angle : 0.483 7.245 20538 Z= 0.242 Chirality : 0.039 0.153 2443 Planarity : 0.004 0.037 2520 Dihedral : 7.590 53.387 2212 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.48 % Allowed : 9.03 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1897 helix: 1.93 (0.16), residues: 1099 sheet: -2.08 (0.27), residues: 280 loop : -2.68 (0.20), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 253 HIS 0.001 0.000 HIS A 484 PHE 0.005 0.001 PHE B 222 TYR 0.008 0.001 TYR D 238 ARG 0.002 0.000 ARG F 265 *********************** 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 153 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 410 ASP cc_start: 0.7128 (t0) cc_final: 0.6914 (t0) REVERT: F 461 MET cc_start: 0.7850 (ptp) cc_final: 0.7627 (ptm) outliers start: 24 outliers final: 12 residues processed: 147 average time/residue: 0.2017 time to fit residues: 48.8944 Evaluate side-chains 131 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 354 SER 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 95 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 185 optimal weight: 0.5980 chunk 153 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15274 Z= 0.160 Angle : 0.435 6.404 20538 Z= 0.218 Chirality : 0.039 0.159 2443 Planarity : 0.003 0.032 2520 Dihedral : 6.532 51.493 2212 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.18 % Allowed : 10.64 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.20), residues: 1897 helix: 2.44 (0.16), residues: 1141 sheet: -1.90 (0.27), residues: 273 loop : -2.55 (0.22), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 253 HIS 0.001 0.000 HIS F 439 PHE 0.007 0.001 PHE A 323 TYR 0.004 0.001 TYR C 441 ARG 0.001 0.000 ARG D 444 *********************** 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 148 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.6266 (m-80) REVERT: B 215 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.6601 (m-80) REVERT: D 215 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6265 (m-80) REVERT: E 215 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.6563 (m-80) REVERT: F 215 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.6363 (m-80) REVERT: F 461 MET cc_start: 0.7900 (ptp) cc_final: 0.7472 (ptp) outliers start: 19 outliers final: 13 residues processed: 134 average time/residue: 0.1919 time to fit residues: 43.6185 Evaluate side-chains 141 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 413 MET 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 251 LEU 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 218 THR Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 284 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 15274 Z= 0.371 Angle : 0.533 7.859 20538 Z= 0.267 Chirality : 0.041 0.133 2443 Planarity : 0.003 0.037 2520 Dihedral : 6.561 53.296 2212 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.47 % Allowed : 10.58 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1897 helix: 2.74 (0.16), residues: 1141 sheet: -1.39 (0.29), residues: 273 loop : -2.44 (0.22), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 253 HIS 0.002 0.001 HIS G 484 PHE 0.012 0.001 PHE A 323 TYR 0.006 0.001 TYR D 441 ARG 0.001 0.000 ARG B 426 *********************** 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 170 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 130 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6979 (OUTLIER) cc_final: 0.6484 (m-80) REVERT: B 215 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: B 228 MET cc_start: 0.8065 (ttm) cc_final: 0.7744 (ttm) REVERT: D 215 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6531 (m-80) REVERT: E 215 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6662 (m-80) REVERT: F 215 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.6359 (m-80) REVERT: F 461 MET cc_start: 0.7980 (ptp) cc_final: 0.7604 (ptp) outliers start: 40 outliers final: 32 residues processed: 147 average time/residue: 0.1889 time to fit residues: 47.1801 Evaluate side-chains 162 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 1.818 ------------------------------------------------------------------------------- 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 284 ASP 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 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 284 ASP 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 413 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15274 Z= 0.218 Angle : 0.452 7.457 20538 Z= 0.224 Chirality : 0.039 0.127 2443 Planarity : 0.003 0.032 2520 Dihedral : 6.212 59.905 2212 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.47 % Allowed : 11.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.20), residues: 1897 helix: 2.94 (0.16), residues: 1141 sheet: -1.12 (0.30), residues: 273 loop : -2.36 (0.23), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 253 HIS 0.001 0.000 HIS G 484 PHE 0.008 0.001 PHE A 323 TYR 0.004 0.001 TYR B 238 ARG 0.001 0.000 ARG D 426 *********************** 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 173 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 133 time to evaluate : 1.604 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6946 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: A 267 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8615 (tt) REVERT: B 215 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: B 267 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8588 (tt) REVERT: D 215 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.6547 (m-80) REVERT: E 215 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: F 215 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6315 (m-80) outliers start: 40 outliers final: 26 residues processed: 152 average time/residue: 0.1840 time to fit residues: 47.5999 Evaluate side-chains 163 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 130 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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 267 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 413 MET 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 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 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 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 250 SER Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 284 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 0.0070 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2534 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= 0.125 Angle : 0.418 7.110 20538 Z= 0.204 Chirality : 0.038 0.123 2443 Planarity : 0.003 0.028 2520 Dihedral : 5.804 57.619 2212 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.36 % Allowed : 13.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.20), residues: 1897 helix: 3.41 (0.15), residues: 1099 sheet: -0.71 (0.31), residues: 280 loop : -1.87 (0.23), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 253 HIS 0.001 0.000 HIS F 439 PHE 0.004 0.001 PHE B 323 TYR 0.003 0.000 TYR G 441 ARG 0.001 0.000 ARG A 426 *********************** 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 159 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.642 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.6460 (m-80) REVERT: B 215 TYR cc_start: 0.7219 (OUTLIER) cc_final: 0.6740 (m-80) REVERT: D 215 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.6519 (m-80) REVERT: E 215 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.6584 (m-80) REVERT: F 215 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6341 (m-80) outliers start: 22 outliers final: 16 residues processed: 150 average time/residue: 0.1932 time to fit residues: 48.8683 Evaluate side-chains 157 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 388 VAL 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 284 ASP Chi-restraints excluded: chain C residue 413 MET 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 E residue 445 VAL 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 F residue 445 VAL Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 250 SER Chi-restraints excluded: chain G residue 388 VAL 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 176 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 182 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15274 Z= 0.139 Angle : 0.418 6.660 20538 Z= 0.204 Chirality : 0.038 0.127 2443 Planarity : 0.003 0.024 2520 Dihedral : 5.587 59.264 2212 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.36 % Allowed : 13.17 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.20), residues: 1897 helix: 3.53 (0.15), residues: 1099 sheet: -0.58 (0.33), residues: 287 loop : -1.72 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 253 HIS 0.001 0.000 HIS F 439 PHE 0.006 0.001 PHE A 323 TYR 0.003 0.000 TYR C 441 ARG 0.001 0.000 ARG B 426 *********************** 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 161 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 1.700 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6942 (OUTLIER) cc_final: 0.6513 (m-80) REVERT: A 267 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8639 (tt) REVERT: B 215 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6700 (m-80) REVERT: B 267 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8583 (tt) REVERT: D 215 TYR cc_start: 0.7190 (OUTLIER) cc_final: 0.6505 (m-80) REVERT: E 215 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6618 (m-80) REVERT: F 215 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.6299 (m-80) outliers start: 22 outliers final: 14 residues processed: 152 average time/residue: 0.2027 time to fit residues: 52.4107 Evaluate side-chains 159 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 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 445 VAL 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 D residue 215 TYR Chi-restraints excluded: chain E residue 215 TYR 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 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 445 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15274 Z= 0.268 Angle : 0.469 7.336 20538 Z= 0.231 Chirality : 0.040 0.132 2443 Planarity : 0.003 0.028 2520 Dihedral : 5.974 57.492 2212 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.73 % Allowed : 12.80 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.20), residues: 1897 helix: 3.57 (0.15), residues: 1099 sheet: -0.40 (0.33), residues: 287 loop : -1.71 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 253 HIS 0.001 0.000 HIS G 484 PHE 0.010 0.001 PHE A 323 TYR 0.004 0.001 TYR D 441 ARG 0.001 0.000 ARG G 426 *********************** 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 166 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6933 (OUTLIER) cc_final: 0.6547 (m-80) REVERT: A 267 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8676 (tt) REVERT: B 215 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: B 267 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8596 (tt) REVERT: D 215 TYR cc_start: 0.7199 (OUTLIER) cc_final: 0.6528 (m-80) REVERT: E 215 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.6605 (m-80) REVERT: F 215 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.6284 (m-80) outliers start: 28 outliers final: 20 residues processed: 155 average time/residue: 0.1856 time to fit residues: 49.0302 Evaluate side-chains 162 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 267 LEU 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 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 250 SER Chi-restraints excluded: chain E residue 215 TYR 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 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 388 VAL 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 174 optimal weight: 0.3980 chunk 159 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 153 optimal weight: 0.3980 chunk 160 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2709 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= 0.141 Angle : 0.422 7.225 20538 Z= 0.206 Chirality : 0.038 0.125 2443 Planarity : 0.003 0.025 2520 Dihedral : 5.623 59.782 2212 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.36 % Allowed : 13.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.20), residues: 1897 helix: 3.61 (0.15), residues: 1099 sheet: -0.36 (0.33), residues: 287 loop : -1.69 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 253 HIS 0.000 0.000 HIS G 484 PHE 0.006 0.001 PHE D 323 TYR 0.003 0.000 TYR B 441 ARG 0.000 0.000 ARG E 326 *********************** 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 160 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 1.721 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.6520 (m-80) REVERT: A 267 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8652 (tt) REVERT: B 215 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.6727 (m-80) REVERT: B 267 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8608 (tt) REVERT: D 215 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.6563 (m-80) REVERT: D 228 MET cc_start: 0.8132 (ttm) cc_final: 0.7783 (ttm) REVERT: E 215 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: F 215 TYR cc_start: 0.7168 (OUTLIER) cc_final: 0.6309 (m-80) outliers start: 22 outliers final: 13 residues processed: 151 average time/residue: 0.1869 time to fit residues: 47.7984 Evaluate side-chains 156 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 267 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 445 VAL Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 413 MET 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 413 MET 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 109 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 159 optimal weight: 0.0770 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15274 Z= 0.163 Angle : 0.428 6.950 20538 Z= 0.209 Chirality : 0.038 0.126 2443 Planarity : 0.003 0.025 2520 Dihedral : 5.560 59.812 2212 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.36 % Allowed : 13.30 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.20), residues: 1897 helix: 3.68 (0.15), residues: 1099 sheet: -0.27 (0.34), residues: 287 loop : -1.63 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 253 HIS 0.001 0.000 HIS E 484 PHE 0.006 0.001 PHE C 323 TYR 0.003 0.000 TYR C 441 ARG 0.000 0.000 ARG B 426 ********************** 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 160 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 1.796 Fit side-chains revert: symmetry clash REVERT: A 215 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.6511 (m-80) REVERT: A 267 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8694 (tt) REVERT: B 215 TYR cc_start: 0.7164 (OUTLIER) cc_final: 0.6690 (m-80) REVERT: B 267 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8622 (tt) REVERT: D 215 TYR cc_start: 0.7175 (OUTLIER) cc_final: 0.6551 (m-80) REVERT: D 228 MET cc_start: 0.8143 (ttm) cc_final: 0.7803 (ttm) REVERT: E 215 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.6625 (m-80) REVERT: E 305 VAL cc_start: 0.8636 (m) cc_final: 0.8435 (m) REVERT: F 215 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6312 (m-80) outliers start: 22 outliers final: 15 residues processed: 151 average time/residue: 0.1891 time to fit residues: 48.8532 Evaluate side-chains 160 residues out of total 1617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 TYR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 267 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 250 SER Chi-restraints excluded: chain C residue 413 MET 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 E residue 311 LEU 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 413 MET 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 45 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 27 optimal weight: 20.0000 chunk 131 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.086375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.063137 restraints weight = 32764.648| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.16 r_work: 0.2682 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2687 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= 0.250 Angle : 0.465 7.339 20538 Z= 0.229 Chirality : 0.039 0.129 2443 Planarity : 0.003 0.027 2520 Dihedral : 5.849 54.309 2212 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.55 % Allowed : 13.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.20), residues: 1897 helix: 3.70 (0.15), residues: 1099 sheet: -0.21 (0.34), residues: 287 loop : -1.67 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 253 HIS 0.001 0.000 HIS G 484 PHE 0.009 0.001 PHE A 323 TYR 0.004 0.001 TYR C 256 ARG 0.001 0.000 ARG A 426 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2377.05 seconds wall clock time: 43 minutes 57.12 seconds (2637.12 seconds total)