Starting phenix.real_space_refine on Thu Sep 26 20:08:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/09_2024/7rsh_24670.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/09_2024/7rsh_24670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/09_2024/7rsh_24670.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/09_2024/7rsh_24670.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/09_2024/7rsh_24670.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsh_24670/09_2024/7rsh_24670.cif" } resolution = 3.0 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 9244 2.51 5 N 2148 2.21 5 O 2316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13744 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3191 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 25, 'TRANS': 375} Chain breaks: 1 Chain: "D" Number of atoms: 3191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3191 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 25, 'TRANS': 375} Chain breaks: 1 Chain: "A" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'PGW': 14} Classifications: {'RNA': 1, 'undetermined': 14} Modifications used: {'rna3p': 1} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PGW:plan-1': 12, 'PGW:plan-2': 12, 'PGW:plan-3': 8} Unresolved non-hydrogen planarities: 119 Chain: "D" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'PGW': 14} Classifications: {'RNA': 1, 'undetermined': 14} Modifications used: {'rna3p': 1} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 491 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'PGW:plan-1': 12, 'PGW:plan-2': 12, 'PGW:plan-3': 8} Unresolved non-hydrogen planarities: 119 Restraints were copied for chains: B, C Time building chain proxies: 8.91, per 1000 atoms: 0.65 Number of scatterers: 13744 At special positions: 0 Unit cell: (106.937, 106.937, 123.877, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 8 15.00 O 2316 8.00 N 2148 7.00 C 9244 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: 3.12 Conformation dependent library (CDL) restraints added in 1.6 seconds 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 8 sheets defined 64.8% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 14 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 43 through 63 removed outlier: 4.385A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.617A pdb=" N LEU A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 101 through 106 removed outlier: 4.081A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.940A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.962A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 removed outlier: 3.588A pdb=" N LEU A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 223 Processing helix chain 'A' and resid 227 through 246 Processing helix chain 'A' and resid 249 through 268 removed outlier: 3.727A pdb=" N ILE A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.940A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 4.310A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 404 through 417 removed outlier: 3.627A pdb=" N ARG A 417 " --> pdb=" O GLU A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 43 through 63 removed outlier: 4.385A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.617A pdb=" N LEU B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 101 through 106 removed outlier: 4.080A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.940A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.962A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 removed outlier: 3.588A pdb=" N LEU B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 223 Processing helix chain 'B' and resid 227 through 246 Processing helix chain 'B' and resid 249 through 268 removed outlier: 3.727A pdb=" N ILE B 257 " --> pdb=" O GLN B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.940A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 4.310A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 404 through 417 removed outlier: 3.627A pdb=" N ARG B 417 " --> pdb=" O GLU B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 43 through 63 removed outlier: 4.385A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.617A pdb=" N LEU C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 101 through 106 removed outlier: 4.080A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.941A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.963A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 158 removed outlier: 3.589A pdb=" N LEU C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 223 Processing helix chain 'C' and resid 227 through 246 Processing helix chain 'C' and resid 249 through 268 removed outlier: 3.727A pdb=" N ILE C 257 " --> pdb=" O GLN C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.940A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 4.311A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 404 through 417 removed outlier: 3.627A pdb=" N ARG C 417 " --> pdb=" O GLU C 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 43 through 63 removed outlier: 4.386A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.618A pdb=" N LEU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 101 through 106 removed outlier: 4.081A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.940A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 removed outlier: 3.962A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 removed outlier: 3.589A pdb=" N LEU D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 158 " --> pdb=" O GLY D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 223 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 249 through 268 removed outlier: 3.727A pdb=" N ILE D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.940A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 4.310A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 404 through 417 removed outlier: 3.627A pdb=" N ARG D 417 " --> pdb=" O GLU D 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.961A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 329 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 320 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.960A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 329 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 320 Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.961A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 329 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 320 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.960A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 329 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 752 hydrogen bonds defined for protein. 2184 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: 3.85 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1992 1.31 - 1.43: 3463 1.43 - 1.56: 8473 1.56 - 1.68: 16 1.68 - 1.80: 48 Bond restraints: 13992 Sorted by residual: bond pdb=" C10 PGW D 515 " pdb=" C9 PGW D 515 " ideal model delta sigma weight residual 1.333 1.529 -0.196 2.00e-02 2.50e+03 9.63e+01 bond pdb=" C10 PGW A 514 " pdb=" C9 PGW A 514 " ideal model delta sigma weight residual 1.333 1.529 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C10 PGW B 514 " pdb=" C9 PGW B 514 " ideal model delta sigma weight residual 1.333 1.529 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C10 PGW C 514 " pdb=" C9 PGW C 514 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" C10 PGW B 509 " pdb=" C9 PGW B 509 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.52e+01 ... (remaining 13987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 18281 3.92 - 7.84: 399 7.84 - 11.76: 40 11.76 - 15.68: 4 15.68 - 19.59: 36 Bond angle restraints: 18760 Sorted by residual: angle pdb=" C06 PGW D 511 " pdb=" C10 PGW D 511 " pdb=" C9 PGW D 511 " ideal model delta sigma weight residual 126.92 107.33 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C06 PGW A 510 " pdb=" C10 PGW A 510 " pdb=" C9 PGW A 510 " ideal model delta sigma weight residual 126.92 107.33 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C06 PGW B 510 " pdb=" C10 PGW B 510 " pdb=" C9 PGW B 510 " ideal model delta sigma weight residual 126.92 107.33 19.59 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C06 PGW C 510 " pdb=" C10 PGW C 510 " pdb=" C9 PGW C 510 " ideal model delta sigma weight residual 126.92 107.37 19.55 3.00e+00 1.11e-01 4.25e+01 angle pdb=" C06 PGW D 504 " pdb=" C10 PGW D 504 " pdb=" C9 PGW D 504 " ideal model delta sigma weight residual 126.92 108.41 18.51 3.00e+00 1.11e-01 3.81e+01 ... (remaining 18755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 8272 33.70 - 67.40: 288 67.40 - 101.10: 20 101.10 - 134.80: 20 134.80 - 168.50: 12 Dihedral angle restraints: 8612 sinusoidal: 3896 harmonic: 4716 Sorted by residual: dihedral pdb=" C5' CMP B 501 " pdb=" O5' CMP B 501 " pdb=" P CMP B 501 " pdb=" O1P CMP B 501 " ideal model delta sinusoidal sigma weight residual 60.00 168.92 -108.92 1 2.00e+01 2.50e-03 3.18e+01 dihedral pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 168.89 -108.89 1 2.00e+01 2.50e-03 3.18e+01 dihedral pdb=" C5' CMP D 502 " pdb=" O5' CMP D 502 " pdb=" P CMP D 502 " pdb=" O1P CMP D 502 " ideal model delta sinusoidal sigma weight residual 60.00 168.86 -108.86 1 2.00e+01 2.50e-03 3.18e+01 ... (remaining 8609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1408 0.041 - 0.081: 519 0.081 - 0.122: 205 0.122 - 0.162: 12 0.162 - 0.203: 4 Chirality restraints: 2148 Sorted by residual: chirality pdb=" C02 PGW C 502 " pdb=" C01 PGW C 502 " pdb=" C03 PGW C 502 " pdb=" O01 PGW C 502 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C02 PGW D 503 " pdb=" C01 PGW D 503 " pdb=" C03 PGW D 503 " pdb=" O01 PGW D 503 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C02 PGW B 502 " pdb=" C01 PGW B 502 " pdb=" C03 PGW B 502 " pdb=" O01 PGW B 502 " both_signs ideal model delta sigma weight residual False 2.36 2.56 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2145 not shown) Planarity restraints: 2248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 503 " 0.109 2.00e-02 2.50e+03 3.57e-01 1.27e+03 pdb=" C10 PGW A 503 " 0.136 2.00e-02 2.50e+03 pdb=" C8 PGW A 503 " 0.351 2.00e-02 2.50e+03 pdb=" C9 PGW A 503 " -0.596 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 503 " 0.109 2.00e-02 2.50e+03 3.57e-01 1.27e+03 pdb=" C10 PGW B 503 " 0.136 2.00e-02 2.50e+03 pdb=" C8 PGW B 503 " 0.351 2.00e-02 2.50e+03 pdb=" C9 PGW B 503 " -0.596 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 504 " -0.112 2.00e-02 2.50e+03 3.57e-01 1.27e+03 pdb=" C10 PGW D 504 " -0.132 2.00e-02 2.50e+03 pdb=" C8 PGW D 504 " -0.352 2.00e-02 2.50e+03 pdb=" C9 PGW D 504 " 0.596 2.00e-02 2.50e+03 ... (remaining 2245 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2010 2.76 - 3.29: 12733 3.29 - 3.83: 21149 3.83 - 4.36: 26144 4.36 - 4.90: 44892 Nonbonded interactions: 106928 Sorted by model distance: nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR A 180 " pdb=" OH TYR D 186 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR C 186 " pdb=" OG1 THR D 180 " model vdw 2.249 3.040 nonbonded pdb=" NH2 ARG B 238 " pdb=" OE2 GLU C 278 " model vdw 2.267 3.120 ... (remaining 106923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 418 or (resid 503 and (name C06 or name C07 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or \ (resid 505 and (name C20 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27)) or (resid 506 and (name C15 or name C22 or name C \ 23 or name C24 or name C25 or name C26 or name C27)) or (resid 507 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27)) or resid 509 thro \ ugh 510 or (resid 512 and (name C15 or name C16 or name C17 or name C18 or name \ C25 or name C26 or name C27)) or (resid 513 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'B' and (resid 10 through 418 or (resid 503 and (name C06 or name C07 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or \ (resid 505 and (name C20 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27)) or (resid 506 and (name C15 or name C22 or name C \ 23 or name C24 or name C25 or name C26 or name C27)) or (resid 507 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27)) or resid 509 thro \ ugh 510 or (resid 512 and (name C15 or name C16 or name C17 or name C18 or name \ C25 or name C26 or name C27)) or (resid 513 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'C' and (resid 10 through 418 or (resid 503 and (name C06 or name C07 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or \ (resid 505 and (name C20 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27)) or (resid 506 and (name C15 or name C22 or name C \ 23 or name C24 or name C25 or name C26 or name C27)) or (resid 507 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27)) or resid 509 thro \ ugh 510 or (resid 512 and (name C15 or name C16 or name C17 or name C18 or name \ C25 or name C26 or name C27)) or (resid 513 and (name C15 or name C16 or name C1 \ 7 or name C18 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'D' and (resid 10 through 418 or (resid 503 and (name C06 or name C07 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or \ (resid 505 and (name C20 or name C21 or name C22 or name C23 or name C24 or name \ C25 or name C26 or name C27)) or (resid 506 and (name C15 or name C22 or name C \ 23 or name C24 or name C25 or name C26 or name C27)) or (resid 507 and (name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27)) or resid 509 thro \ ugh 510 or (resid 512 and (name C15 or name C16 or name C17 or name C18 or name \ C25 or name C26 or name C27)) or resid 513)) } 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 31.160 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 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:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.196 13992 Z= 0.597 Angle : 1.428 19.594 18760 Z= 0.569 Chirality : 0.047 0.203 2148 Planarity : 0.017 0.357 2248 Dihedral : 19.070 168.500 5564 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.58 % Allowed : 0.07 % Favored : 99.35 % 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: -0.72 (0.22), residues: 1588 helix: 0.10 (0.17), residues: 1004 sheet: -0.50 (0.56), residues: 88 loop : -1.48 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 264 HIS 0.002 0.001 HIS C 149 PHE 0.018 0.002 PHE C 64 TYR 0.008 0.001 TYR C 170 ARG 0.006 0.001 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 1.385 Fit side-chains REVERT: A 330 ARG cc_start: 0.7096 (mtt90) cc_final: 0.6623 (mtm-85) REVERT: B 330 ARG cc_start: 0.7097 (mtt90) cc_final: 0.6593 (mtm-85) REVERT: C 330 ARG cc_start: 0.7058 (mtt90) cc_final: 0.6605 (mtm-85) REVERT: D 327 TYR cc_start: 0.7900 (m-10) cc_final: 0.7134 (m-80) REVERT: D 330 ARG cc_start: 0.7055 (mtt90) cc_final: 0.6630 (mtm-85) REVERT: D 403 ARG cc_start: 0.7457 (mtt180) cc_final: 0.7057 (mtt180) outliers start: 8 outliers final: 2 residues processed: 184 average time/residue: 1.3385 time to fit residues: 268.4942 Evaluate side-chains 147 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 276 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 0.1980 chunk 125 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 145 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7622 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13992 Z= 0.196 Angle : 0.681 8.645 18760 Z= 0.317 Chirality : 0.041 0.131 2148 Planarity : 0.006 0.086 2248 Dihedral : 18.214 159.812 2528 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.71 % Allowed : 10.90 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1588 helix: 0.70 (0.18), residues: 1016 sheet: -0.32 (0.58), residues: 88 loop : -1.30 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 264 HIS 0.003 0.001 HIS D 232 PHE 0.013 0.001 PHE A 64 TYR 0.006 0.001 TYR D 175 ARG 0.004 0.000 ARG C 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 139 time to evaluate : 1.423 Fit side-chains REVERT: A 156 MET cc_start: 0.7995 (ttp) cc_final: 0.7778 (ttm) REVERT: A 203 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8060 (mp) REVERT: A 273 ARG cc_start: 0.7744 (ptt90) cc_final: 0.7384 (ptp90) REVERT: A 330 ARG cc_start: 0.7192 (mtt90) cc_final: 0.6776 (ttm-80) REVERT: A 333 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: A 337 ASP cc_start: 0.8124 (m-30) cc_final: 0.7897 (m-30) REVERT: B 156 MET cc_start: 0.8010 (ttp) cc_final: 0.7781 (ttm) REVERT: B 203 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8049 (mp) REVERT: B 273 ARG cc_start: 0.7771 (ptt90) cc_final: 0.7400 (ptp90) REVERT: B 337 ASP cc_start: 0.8127 (m-30) cc_final: 0.7903 (m-30) REVERT: C 156 MET cc_start: 0.8000 (ttp) cc_final: 0.7783 (ttm) REVERT: C 203 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8056 (mp) REVERT: C 273 ARG cc_start: 0.7749 (ptt90) cc_final: 0.7390 (ptp90) REVERT: C 337 ASP cc_start: 0.8159 (m-30) cc_final: 0.7923 (m-30) REVERT: D 156 MET cc_start: 0.7999 (ttp) cc_final: 0.7778 (ttm) REVERT: D 203 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8027 (mp) REVERT: D 273 ARG cc_start: 0.7712 (ptt90) cc_final: 0.7340 (ptp90) REVERT: D 333 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7365 (mp0) outliers start: 51 outliers final: 8 residues processed: 167 average time/residue: 1.3190 time to fit residues: 240.4789 Evaluate side-chains 143 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 333 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 145 optimal weight: 0.0770 chunk 157 optimal weight: 3.9990 chunk 129 optimal weight: 0.0270 chunk 144 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 overall best weight: 1.4200 ------------------------------------------------------------------------------- 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: 0.7665 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13992 Z= 0.290 Angle : 0.685 8.194 18760 Z= 0.324 Chirality : 0.043 0.134 2148 Planarity : 0.006 0.065 2248 Dihedral : 17.566 159.330 2524 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.94 % Allowed : 13.15 % Favored : 81.90 % 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: 0.46 (0.23), residues: 1588 helix: 1.07 (0.18), residues: 960 sheet: -0.13 (0.57), residues: 88 loop : -0.92 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 264 HIS 0.004 0.001 HIS D 149 PHE 0.006 0.001 PHE A 260 TYR 0.008 0.001 TYR D 170 ARG 0.002 0.000 ARG C 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 135 time to evaluate : 1.454 Fit side-chains REVERT: A 273 ARG cc_start: 0.7691 (ptt90) cc_final: 0.7255 (ptp90) REVERT: A 327 TYR cc_start: 0.7844 (m-10) cc_final: 0.7031 (m-80) REVERT: A 330 ARG cc_start: 0.7138 (mtt90) cc_final: 0.6703 (ttm-80) REVERT: A 333 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: B 273 ARG cc_start: 0.7691 (ptt90) cc_final: 0.7261 (ptp90) REVERT: B 327 TYR cc_start: 0.7869 (m-10) cc_final: 0.7042 (m-80) REVERT: B 330 ARG cc_start: 0.7140 (mtt90) cc_final: 0.6813 (ttm-80) REVERT: C 273 ARG cc_start: 0.7681 (ptt90) cc_final: 0.7263 (ptp90) REVERT: C 327 TYR cc_start: 0.7844 (m-10) cc_final: 0.7036 (m-80) REVERT: C 330 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6804 (ttm-80) REVERT: C 403 ARG cc_start: 0.7261 (mtt180) cc_final: 0.7039 (mtt180) REVERT: D 273 ARG cc_start: 0.7701 (ptt90) cc_final: 0.7249 (ptp90) REVERT: D 327 TYR cc_start: 0.7851 (m-10) cc_final: 0.7047 (m-80) REVERT: D 333 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: D 403 ARG cc_start: 0.7272 (mtt180) cc_final: 0.7047 (mtt180) outliers start: 68 outliers final: 20 residues processed: 182 average time/residue: 1.3431 time to fit residues: 269.6019 Evaluate side-chains 151 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 0.0970 chunk 154 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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: 0.7623 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13992 Z= 0.194 Angle : 0.635 7.891 18760 Z= 0.296 Chirality : 0.041 0.167 2148 Planarity : 0.005 0.056 2248 Dihedral : 16.730 157.506 2524 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.92 % Allowed : 14.53 % Favored : 81.54 % 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: 0.81 (0.23), residues: 1588 helix: 1.35 (0.18), residues: 964 sheet: 0.17 (0.60), residues: 88 loop : -0.83 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 264 HIS 0.002 0.001 HIS A 232 PHE 0.008 0.001 PHE B 40 TYR 0.006 0.001 TYR B 175 ARG 0.002 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 156 time to evaluate : 1.569 Fit side-chains REVERT: A 77 LEU cc_start: 0.2971 (OUTLIER) cc_final: 0.2528 (tt) REVERT: A 203 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8097 (mp) REVERT: A 273 ARG cc_start: 0.7617 (ptt90) cc_final: 0.7161 (mtm-85) REVERT: A 327 TYR cc_start: 0.7836 (m-10) cc_final: 0.7066 (m-80) REVERT: A 330 ARG cc_start: 0.7111 (mtt90) cc_final: 0.6688 (ttm-80) REVERT: A 333 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: B 77 LEU cc_start: 0.2986 (OUTLIER) cc_final: 0.2531 (tt) REVERT: B 203 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8094 (mp) REVERT: B 273 ARG cc_start: 0.7639 (ptt90) cc_final: 0.7181 (mtm-85) REVERT: B 330 ARG cc_start: 0.7127 (mtt90) cc_final: 0.6709 (ttm-80) REVERT: C 77 LEU cc_start: 0.2983 (OUTLIER) cc_final: 0.2523 (tt) REVERT: C 203 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8095 (mp) REVERT: C 273 ARG cc_start: 0.7624 (ptt90) cc_final: 0.7150 (mtm-85) REVERT: C 330 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6671 (ttm-80) REVERT: D 77 LEU cc_start: 0.2950 (OUTLIER) cc_final: 0.2492 (tt) REVERT: D 203 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8098 (mp) REVERT: D 273 ARG cc_start: 0.7630 (ptt90) cc_final: 0.7154 (mtm-85) REVERT: D 327 TYR cc_start: 0.7800 (m-10) cc_final: 0.7019 (m-80) REVERT: D 330 ARG cc_start: 0.7143 (mtt90) cc_final: 0.6781 (mtm-85) REVERT: D 333 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7291 (mp0) outliers start: 54 outliers final: 10 residues processed: 194 average time/residue: 1.1433 time to fit residues: 244.8669 Evaluate side-chains 158 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 115 optimal weight: 0.0060 chunk 63 optimal weight: 0.0970 chunk 131 optimal weight: 0.9990 chunk 106 optimal weight: 0.0010 chunk 0 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13992 Z= 0.161 Angle : 0.605 7.938 18760 Z= 0.281 Chirality : 0.040 0.128 2148 Planarity : 0.005 0.054 2248 Dihedral : 15.796 155.560 2524 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.12 % Allowed : 17.01 % Favored : 79.87 % 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: 1.10 (0.23), residues: 1588 helix: 1.53 (0.18), residues: 972 sheet: 0.38 (0.62), residues: 88 loop : -0.68 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 264 HIS 0.001 0.000 HIS D 232 PHE 0.007 0.001 PHE D 40 TYR 0.006 0.001 TYR D 175 ARG 0.002 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 150 time to evaluate : 1.432 Fit side-chains REVERT: A 44 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.5727 (mm) REVERT: A 77 LEU cc_start: 0.2778 (OUTLIER) cc_final: 0.2366 (tt) REVERT: A 203 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8145 (mp) REVERT: A 273 ARG cc_start: 0.7662 (ptt90) cc_final: 0.7196 (mtm-85) REVERT: A 330 ARG cc_start: 0.7062 (mtt90) cc_final: 0.6620 (ttm-80) REVERT: A 333 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: B 44 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5733 (mm) REVERT: B 77 LEU cc_start: 0.2966 (OUTLIER) cc_final: 0.2544 (tt) REVERT: B 203 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8145 (mp) REVERT: B 273 ARG cc_start: 0.7663 (ptt90) cc_final: 0.7201 (mtm-85) REVERT: B 330 ARG cc_start: 0.7128 (mtt90) cc_final: 0.6850 (mtm-85) REVERT: C 44 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5732 (mm) REVERT: C 77 LEU cc_start: 0.2888 (OUTLIER) cc_final: 0.2463 (tt) REVERT: C 203 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8144 (mp) REVERT: C 273 ARG cc_start: 0.7653 (ptt90) cc_final: 0.7184 (mtm-85) REVERT: C 330 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6764 (ttm-80) REVERT: D 44 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5717 (mm) REVERT: D 77 LEU cc_start: 0.2837 (OUTLIER) cc_final: 0.2415 (tt) REVERT: D 203 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8141 (mp) REVERT: D 273 ARG cc_start: 0.7676 (ptt90) cc_final: 0.7208 (mtm-85) REVERT: D 327 TYR cc_start: 0.7774 (m-10) cc_final: 0.7039 (m-80) REVERT: D 330 ARG cc_start: 0.7132 (mtt90) cc_final: 0.6817 (ttm-80) outliers start: 43 outliers final: 10 residues processed: 175 average time/residue: 1.3771 time to fit residues: 262.1237 Evaluate side-chains 162 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.7652 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13992 Z= 0.272 Angle : 0.651 8.209 18760 Z= 0.307 Chirality : 0.043 0.133 2148 Planarity : 0.005 0.056 2248 Dihedral : 16.251 153.820 2524 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.07 % Allowed : 17.22 % Favored : 78.71 % 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: 0.95 (0.23), residues: 1588 helix: 1.43 (0.18), residues: 968 sheet: 0.26 (0.60), residues: 88 loop : -0.74 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 176 HIS 0.003 0.001 HIS B 149 PHE 0.006 0.001 PHE D 260 TYR 0.009 0.001 TYR A 170 ARG 0.002 0.000 ARG D 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 133 time to evaluate : 1.345 Fit side-chains REVERT: A 44 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5877 (mm) REVERT: A 77 LEU cc_start: 0.2770 (OUTLIER) cc_final: 0.2373 (tt) REVERT: A 273 ARG cc_start: 0.7678 (ptt90) cc_final: 0.7174 (mtm-85) REVERT: A 327 TYR cc_start: 0.7822 (m-10) cc_final: 0.7128 (m-80) REVERT: A 330 ARG cc_start: 0.7077 (mtt90) cc_final: 0.6599 (ttm-80) REVERT: A 333 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: B 44 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5879 (mm) REVERT: B 77 LEU cc_start: 0.2779 (OUTLIER) cc_final: 0.2377 (tt) REVERT: B 273 ARG cc_start: 0.7687 (ptt90) cc_final: 0.7176 (mtm-85) REVERT: B 327 TYR cc_start: 0.7829 (m-10) cc_final: 0.7188 (m-80) REVERT: B 330 ARG cc_start: 0.7117 (mtt90) cc_final: 0.6755 (ttm-80) REVERT: C 44 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5876 (mm) REVERT: C 77 LEU cc_start: 0.2774 (OUTLIER) cc_final: 0.2369 (tt) REVERT: C 273 ARG cc_start: 0.7672 (ptt90) cc_final: 0.7174 (mtm-85) REVERT: C 327 TYR cc_start: 0.7820 (m-10) cc_final: 0.7107 (m-80) REVERT: C 330 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6735 (ttm-80) REVERT: D 44 LEU cc_start: 0.6173 (OUTLIER) cc_final: 0.5871 (mm) REVERT: D 77 LEU cc_start: 0.2725 (OUTLIER) cc_final: 0.2325 (tt) REVERT: D 273 ARG cc_start: 0.7679 (ptt90) cc_final: 0.7187 (mtm-85) REVERT: D 327 TYR cc_start: 0.7824 (m-10) cc_final: 0.7181 (m-80) REVERT: D 330 ARG cc_start: 0.7076 (mtt90) cc_final: 0.6705 (ttm-80) outliers start: 56 outliers final: 17 residues processed: 176 average time/residue: 1.2016 time to fit residues: 232.3764 Evaluate side-chains 157 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 96 optimal weight: 0.1980 chunk 94 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.7679 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13992 Z= 0.349 Angle : 0.697 8.770 18760 Z= 0.330 Chirality : 0.045 0.135 2148 Planarity : 0.005 0.057 2248 Dihedral : 16.471 152.540 2524 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 5.52 % Allowed : 16.64 % Favored : 77.83 % 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: 0.67 (0.22), residues: 1588 helix: 1.19 (0.18), residues: 972 sheet: 0.08 (0.58), residues: 88 loop : -0.81 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 264 HIS 0.003 0.001 HIS B 149 PHE 0.007 0.001 PHE D 260 TYR 0.009 0.002 TYR B 170 ARG 0.003 0.000 ARG C 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 132 time to evaluate : 1.334 Fit side-chains REVERT: A 43 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7393 (mp) REVERT: A 44 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5598 (mm) REVERT: A 77 LEU cc_start: 0.2758 (OUTLIER) cc_final: 0.2382 (tt) REVERT: A 273 ARG cc_start: 0.7617 (ptt90) cc_final: 0.7126 (mtm-85) REVERT: A 327 TYR cc_start: 0.7916 (m-10) cc_final: 0.7330 (m-80) REVERT: A 330 ARG cc_start: 0.7106 (mtt90) cc_final: 0.6641 (ttm-80) REVERT: A 333 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: A 389 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8468 (pp) REVERT: B 43 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7391 (mp) REVERT: B 44 LEU cc_start: 0.6104 (OUTLIER) cc_final: 0.5590 (mm) REVERT: B 77 LEU cc_start: 0.2763 (OUTLIER) cc_final: 0.2385 (tt) REVERT: B 273 ARG cc_start: 0.7623 (ptt90) cc_final: 0.7200 (mtm-85) REVERT: B 327 TYR cc_start: 0.7930 (m-10) cc_final: 0.7333 (m-80) REVERT: B 330 ARG cc_start: 0.7103 (mtt90) cc_final: 0.6717 (ttm-80) REVERT: B 389 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8467 (pp) REVERT: C 43 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7405 (mp) REVERT: C 77 LEU cc_start: 0.2757 (OUTLIER) cc_final: 0.2374 (tt) REVERT: C 273 ARG cc_start: 0.7613 (ptt90) cc_final: 0.7167 (mtm-85) REVERT: C 327 TYR cc_start: 0.7919 (m-10) cc_final: 0.7332 (m-80) REVERT: C 330 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6628 (ttm-80) REVERT: C 389 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8472 (pp) REVERT: D 43 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7391 (mp) REVERT: D 44 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5595 (mm) REVERT: D 77 LEU cc_start: 0.2676 (OUTLIER) cc_final: 0.2302 (tt) REVERT: D 273 ARG cc_start: 0.7615 (ptt90) cc_final: 0.7183 (mtm-85) REVERT: D 318 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7182 (tp30) REVERT: D 330 ARG cc_start: 0.7090 (mtt90) cc_final: 0.6722 (ttm-80) REVERT: D 389 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8480 (pp) outliers start: 76 outliers final: 32 residues processed: 192 average time/residue: 1.1030 time to fit residues: 233.7898 Evaluate side-chains 179 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 129 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 14 optimal weight: 0.0770 chunk 121 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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: 0.7619 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13992 Z= 0.180 Angle : 0.606 8.038 18760 Z= 0.286 Chirality : 0.041 0.127 2148 Planarity : 0.005 0.056 2248 Dihedral : 15.509 151.415 2524 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.56 % Allowed : 18.97 % Favored : 77.47 % 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: 1.06 (0.23), residues: 1588 helix: 1.49 (0.18), residues: 980 sheet: 0.30 (0.60), residues: 88 loop : -0.69 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 264 HIS 0.002 0.001 HIS A 149 PHE 0.009 0.001 PHE B 40 TYR 0.006 0.001 TYR C 245 ARG 0.002 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 133 time to evaluate : 1.356 Fit side-chains REVERT: A 44 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5830 (mm) REVERT: A 77 LEU cc_start: 0.2804 (OUTLIER) cc_final: 0.2455 (tt) REVERT: A 203 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8141 (mp) REVERT: A 273 ARG cc_start: 0.7611 (ptt90) cc_final: 0.7074 (mtm-85) REVERT: A 327 TYR cc_start: 0.7796 (m-10) cc_final: 0.7150 (m-80) REVERT: A 330 ARG cc_start: 0.7048 (mtt90) cc_final: 0.6577 (mtm-85) REVERT: A 333 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: B 44 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5828 (mm) REVERT: B 77 LEU cc_start: 0.2807 (OUTLIER) cc_final: 0.2459 (tt) REVERT: B 203 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8138 (mp) REVERT: B 273 ARG cc_start: 0.7610 (ptt90) cc_final: 0.7125 (mtm-85) REVERT: B 330 ARG cc_start: 0.7086 (mtt90) cc_final: 0.6641 (ttm-80) REVERT: C 44 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5831 (mm) REVERT: C 77 LEU cc_start: 0.2805 (OUTLIER) cc_final: 0.2458 (tt) REVERT: C 203 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8139 (mp) REVERT: C 273 ARG cc_start: 0.7586 (ptt90) cc_final: 0.7031 (mtm-85) REVERT: C 327 TYR cc_start: 0.7808 (m-10) cc_final: 0.7104 (m-80) REVERT: C 330 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6432 (ttm-80) REVERT: D 44 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5826 (mm) REVERT: D 77 LEU cc_start: 0.2687 (OUTLIER) cc_final: 0.2323 (tt) REVERT: D 203 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8140 (mp) REVERT: D 273 ARG cc_start: 0.7601 (ptt90) cc_final: 0.7093 (mtm-85) outliers start: 49 outliers final: 12 residues processed: 171 average time/residue: 1.0712 time to fit residues: 202.0332 Evaluate side-chains 159 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 94 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7617 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13992 Z= 0.185 Angle : 0.620 9.120 18760 Z= 0.289 Chirality : 0.041 0.130 2148 Planarity : 0.005 0.056 2248 Dihedral : 15.269 150.035 2524 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.76 % Allowed : 20.78 % Favored : 76.45 % 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: 1.17 (0.23), residues: 1588 helix: 1.56 (0.18), residues: 984 sheet: 0.39 (0.61), residues: 88 loop : -0.63 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 264 HIS 0.002 0.001 HIS D 232 PHE 0.006 0.001 PHE A 366 TYR 0.006 0.001 TYR B 170 ARG 0.002 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 1.351 Fit side-chains REVERT: A 77 LEU cc_start: 0.2759 (OUTLIER) cc_final: 0.2425 (tt) REVERT: A 203 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8070 (mp) REVERT: A 273 ARG cc_start: 0.7574 (ptt90) cc_final: 0.7059 (mtm-85) REVERT: A 327 TYR cc_start: 0.7788 (m-10) cc_final: 0.7152 (m-80) REVERT: A 330 ARG cc_start: 0.7029 (mtt90) cc_final: 0.6522 (ttm-80) REVERT: A 333 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: B 77 LEU cc_start: 0.2766 (OUTLIER) cc_final: 0.2429 (tt) REVERT: B 203 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8068 (mp) REVERT: B 273 ARG cc_start: 0.7574 (ptt90) cc_final: 0.7067 (mtm-85) REVERT: B 330 ARG cc_start: 0.7165 (mtt90) cc_final: 0.6710 (ttm-80) REVERT: C 77 LEU cc_start: 0.2765 (OUTLIER) cc_final: 0.2425 (tt) REVERT: C 203 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8067 (mp) REVERT: C 273 ARG cc_start: 0.7550 (ptt90) cc_final: 0.7056 (mtm-85) REVERT: C 330 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6775 (ttm-80) REVERT: D 77 LEU cc_start: 0.2770 (OUTLIER) cc_final: 0.2429 (tt) REVERT: D 203 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8068 (mp) REVERT: D 273 ARG cc_start: 0.7592 (ptt90) cc_final: 0.7077 (mtm-85) outliers start: 38 outliers final: 9 residues processed: 161 average time/residue: 1.2949 time to fit residues: 227.5865 Evaluate side-chains 154 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.0170 chunk 92 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 chunk 146 optimal weight: 0.4980 chunk 126 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 0.2980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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: 0.7592 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13992 Z= 0.166 Angle : 0.609 8.547 18760 Z= 0.283 Chirality : 0.041 0.143 2148 Planarity : 0.005 0.056 2248 Dihedral : 14.919 148.529 2524 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.89 % Allowed : 21.88 % Favored : 76.24 % 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: 1.23 (0.23), residues: 1588 helix: 1.64 (0.18), residues: 984 sheet: 0.44 (0.61), residues: 88 loop : -0.70 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.001 0.001 HIS B 232 PHE 0.007 0.001 PHE D 366 TYR 0.006 0.001 TYR C 175 ARG 0.002 0.000 ARG C 391 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 1.354 Fit side-chains REVERT: A 77 LEU cc_start: 0.2741 (OUTLIER) cc_final: 0.2428 (tt) REVERT: A 203 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8142 (mp) REVERT: A 273 ARG cc_start: 0.7544 (ptt90) cc_final: 0.7060 (mtm-85) REVERT: A 327 TYR cc_start: 0.7772 (m-10) cc_final: 0.7159 (m-80) REVERT: A 330 ARG cc_start: 0.7042 (mtt90) cc_final: 0.6561 (ttm-80) REVERT: A 333 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: B 77 LEU cc_start: 0.2752 (OUTLIER) cc_final: 0.2436 (tt) REVERT: B 203 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8140 (mp) REVERT: B 273 ARG cc_start: 0.7531 (ptt90) cc_final: 0.7054 (mtm-85) REVERT: B 330 ARG cc_start: 0.7146 (mtt90) cc_final: 0.6545 (ttm-80) REVERT: C 77 LEU cc_start: 0.2752 (OUTLIER) cc_final: 0.2432 (tt) REVERT: C 203 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8140 (mp) REVERT: C 273 ARG cc_start: 0.7534 (ptt90) cc_final: 0.7042 (mtm-85) REVERT: C 330 ARG cc_start: 0.7103 (mtt90) cc_final: 0.6703 (ttm-80) REVERT: D 77 LEU cc_start: 0.2771 (OUTLIER) cc_final: 0.2442 (tt) REVERT: D 203 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8140 (mp) REVERT: D 273 ARG cc_start: 0.7572 (ptt90) cc_final: 0.7075 (mtm-85) outliers start: 26 outliers final: 6 residues processed: 147 average time/residue: 1.3199 time to fit residues: 211.4464 Evaluate side-chains 140 residues out of total 1376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.185916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.148493 restraints weight = 14590.892| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.94 r_work: 0.3145 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13992 Z= 0.195 Angle : 0.617 8.539 18760 Z= 0.288 Chirality : 0.041 0.129 2148 Planarity : 0.005 0.056 2248 Dihedral : 14.924 147.135 2524 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.25 % Allowed : 22.02 % Favored : 75.73 % 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: 1.23 (0.23), residues: 1588 helix: 1.65 (0.18), residues: 984 sheet: 0.46 (0.61), residues: 88 loop : -0.70 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 264 HIS 0.002 0.001 HIS D 232 PHE 0.006 0.001 PHE B 366 TYR 0.007 0.001 TYR B 170 ARG 0.002 0.000 ARG C 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4461.34 seconds wall clock time: 80 minutes 37.98 seconds (4837.98 seconds total)