Starting phenix.real_space_refine on Fri Sep 27 14:22:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/09_2024/7cr7_30448_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/09_2024/7cr7_30448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/09_2024/7cr7_30448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/09_2024/7cr7_30448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/09_2024/7cr7_30448_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/09_2024/7cr7_30448_trim.cif" } resolution = 3.7 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: 5 Type Number sf(0) Gaussians S 88 5.16 5 C 10384 2.51 5 N 2748 2.21 5 O 2912 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 16136 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2886 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "C" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'FBX': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, D, G, E, F, H Time building chain proxies: 7.35, per 1000 atoms: 0.46 Number of scatterers: 16136 At special positions: 0 Unit cell: (130.806, 130.806, 129.792, 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 88 16.00 F 4 9.00 O 2912 8.00 N 2748 7.00 C 10384 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: 4.44 Conformation dependent library (CDL) restraints added in 2.0 seconds 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 81.5% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 91 through 113 removed outlier: 4.380A pdb=" N TYR A 95 " --> pdb=" O TRP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 4.568A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 162 through 165 removed outlier: 3.906A pdb=" N ARG A 165 " --> pdb=" O LYS A 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 162 through 165' Processing helix chain 'A' and resid 166 through 183 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 252 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 348 removed outlier: 3.867A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 3.901A pdb=" N PHE A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Proline residue: A 335 - end of helix removed outlier: 3.943A pdb=" N ILE A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 367 removed outlier: 4.561A pdb=" N TRP A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 557 Processing helix chain 'A' and resid 562 through 599 Proline residue: A 597 - end of helix Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 66 through 75 Processing helix chain 'F' and resid 76 through 80 Processing helix chain 'F' and resid 82 through 94 removed outlier: 4.607A pdb=" N PHE F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 112 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 139 through 148 removed outlier: 3.550A pdb=" N ALA F 148 " --> pdb=" O GLN F 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 91 through 113 removed outlier: 4.380A pdb=" N TYR B 95 " --> pdb=" O TRP B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 4.567A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 165 removed outlier: 3.906A pdb=" N ARG B 165 " --> pdb=" O LYS B 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 162 through 165' Processing helix chain 'B' and resid 166 through 183 Processing helix chain 'B' and resid 196 through 211 Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 252 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 287 through 348 removed outlier: 3.867A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix removed outlier: 3.901A pdb=" N PHE B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Proline residue: B 335 - end of helix removed outlier: 3.944A pdb=" N ILE B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 367 removed outlier: 4.561A pdb=" N TRP B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 557 Processing helix chain 'B' and resid 562 through 599 Proline residue: B 597 - end of helix Processing helix chain 'C' and resid 7 through 21 Processing helix chain 'C' and resid 30 through 41 Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 66 through 75 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 82 through 94 removed outlier: 4.605A pdb=" N PHE C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 139 through 148 removed outlier: 3.551A pdb=" N ALA C 148 " --> pdb=" O GLN C 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 91 through 113 removed outlier: 4.380A pdb=" N TYR D 95 " --> pdb=" O TRP D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 4.568A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 156 through 161 Processing helix chain 'D' and resid 162 through 165 removed outlier: 3.906A pdb=" N ARG D 165 " --> pdb=" O LYS D 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 162 through 165' Processing helix chain 'D' and resid 166 through 183 Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 252 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 287 through 348 removed outlier: 3.867A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix removed outlier: 3.902A pdb=" N PHE D 329 " --> pdb=" O ARG D 325 " (cutoff:3.500A) Proline residue: D 335 - end of helix removed outlier: 3.944A pdb=" N ILE D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 367 removed outlier: 4.561A pdb=" N TRP D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 557 Processing helix chain 'D' and resid 562 through 599 Proline residue: D 597 - end of helix Processing helix chain 'E' and resid 7 through 21 Processing helix chain 'E' and resid 30 through 41 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 82 through 94 removed outlier: 4.606A pdb=" N PHE E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 139 through 148 removed outlier: 3.550A pdb=" N ALA E 148 " --> pdb=" O GLN E 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 86 Processing helix chain 'G' and resid 91 through 113 removed outlier: 4.380A pdb=" N TYR G 95 " --> pdb=" O TRP G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 148 removed outlier: 4.568A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'G' and resid 156 through 161 Processing helix chain 'G' and resid 162 through 165 removed outlier: 3.905A pdb=" N ARG G 165 " --> pdb=" O LYS G 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 162 through 165' Processing helix chain 'G' and resid 166 through 183 Processing helix chain 'G' and resid 196 through 211 Processing helix chain 'G' and resid 215 through 228 Processing helix chain 'G' and resid 228 through 252 Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 287 through 348 removed outlier: 3.867A pdb=" N THR G 296 " --> pdb=" O LEU G 292 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU G 299 " --> pdb=" O ALA G 295 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Proline residue: G 308 - end of helix removed outlier: 3.901A pdb=" N PHE G 329 " --> pdb=" O ARG G 325 " (cutoff:3.500A) Proline residue: G 335 - end of helix removed outlier: 3.944A pdb=" N ILE G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLN G 341 " --> pdb=" O ALA G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 367 removed outlier: 4.562A pdb=" N TRP G 360 " --> pdb=" O LEU G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 557 Processing helix chain 'G' and resid 562 through 599 Proline residue: G 597 - end of helix Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 66 through 75 Processing helix chain 'H' and resid 76 through 80 Processing helix chain 'H' and resid 82 through 94 removed outlier: 4.606A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 112 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 139 through 148 removed outlier: 3.551A pdb=" N ALA H 148 " --> pdb=" O GLN H 144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'C' and resid 27 through 29 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'E' and resid 27 through 29 Processing sheet with id=AA6, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'H' and resid 27 through 29 Processing sheet with id=AA8, first strand: chain 'H' and resid 100 through 102 1181 hydrogen bonds defined for protein. 3519 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: 4.71 Time building geometry restraints manager: 5.00 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: 2609 1.31 - 1.43: 4630 1.43 - 1.56: 9085 1.56 - 1.69: 4 1.69 - 1.81: 148 Bond restraints: 16476 Sorted by residual: bond pdb=" C17 FBX D1001 " pdb=" C19 FBX D1001 " ideal model delta sigma weight residual 1.381 1.522 -0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C17 FBX A1001 " pdb=" C19 FBX A1001 " ideal model delta sigma weight residual 1.381 1.522 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C17 FBX B1001 " pdb=" C19 FBX B1001 " ideal model delta sigma weight residual 1.381 1.521 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C17 FBX G1001 " pdb=" C19 FBX G1001 " ideal model delta sigma weight residual 1.381 1.521 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C16 FBX A1001 " pdb=" C18 FBX A1001 " ideal model delta sigma weight residual 1.388 1.518 -0.130 2.00e-02 2.50e+03 4.23e+01 ... (remaining 16471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 22016 2.96 - 5.92: 165 5.92 - 8.88: 39 8.88 - 11.85: 0 11.85 - 14.81: 4 Bond angle restraints: 22224 Sorted by residual: angle pdb=" C LEU D 559 " pdb=" N ARG D 560 " pdb=" CA ARG D 560 " ideal model delta sigma weight residual 121.80 106.99 14.81 2.44e+00 1.68e-01 3.68e+01 angle pdb=" C LEU A 559 " pdb=" N ARG A 560 " pdb=" CA ARG A 560 " ideal model delta sigma weight residual 121.80 107.00 14.80 2.44e+00 1.68e-01 3.68e+01 angle pdb=" C LEU G 559 " pdb=" N ARG G 560 " pdb=" CA ARG G 560 " ideal model delta sigma weight residual 121.80 107.00 14.80 2.44e+00 1.68e-01 3.68e+01 angle pdb=" C LEU B 559 " pdb=" N ARG B 560 " pdb=" CA ARG B 560 " ideal model delta sigma weight residual 121.80 107.04 14.76 2.44e+00 1.68e-01 3.66e+01 angle pdb=" CA PRO D 561 " pdb=" N PRO D 561 " pdb=" CD PRO D 561 " ideal model delta sigma weight residual 112.00 106.50 5.50 1.40e+00 5.10e-01 1.54e+01 ... (remaining 22219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.74: 9445 32.74 - 65.47: 219 65.47 - 98.21: 20 98.21 - 130.94: 0 130.94 - 163.68: 4 Dihedral angle restraints: 9688 sinusoidal: 3936 harmonic: 5752 Sorted by residual: dihedral pdb=" C8 FBX D1001 " pdb=" C7 FBX D1001 " pdb=" N4 FBX D1001 " pdb=" C9 FBX D1001 " ideal model delta sinusoidal sigma weight residual -75.46 88.22 -163.68 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C8 FBX G1001 " pdb=" C7 FBX G1001 " pdb=" N4 FBX G1001 " pdb=" C9 FBX G1001 " ideal model delta sinusoidal sigma weight residual -75.46 88.19 -163.65 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C8 FBX A1001 " pdb=" C7 FBX A1001 " pdb=" N4 FBX A1001 " pdb=" C9 FBX A1001 " ideal model delta sinusoidal sigma weight residual -75.46 88.17 -163.63 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 9685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1572 0.034 - 0.068: 630 0.068 - 0.102: 149 0.102 - 0.136: 72 0.136 - 0.169: 5 Chirality restraints: 2428 Sorted by residual: chirality pdb=" CG LEU A 559 " pdb=" CB LEU A 559 " pdb=" CD1 LEU A 559 " pdb=" CD2 LEU A 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CG LEU G 559 " pdb=" CB LEU G 559 " pdb=" CD1 LEU G 559 " pdb=" CD2 LEU G 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CG LEU B 559 " pdb=" CB LEU B 559 " pdb=" CD1 LEU B 559 " pdb=" CD2 LEU B 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 2425 not shown) Planarity restraints: 2804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 560 " -0.042 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO D 561 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 561 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 561 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 560 " 0.042 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO G 561 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO G 561 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 561 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 560 " 0.042 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO A 561 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.034 5.00e-02 4.00e+02 ... (remaining 2801 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 355 2.55 - 3.14: 17121 3.14 - 3.72: 28153 3.72 - 4.31: 40282 4.31 - 4.90: 58057 Nonbonded interactions: 143968 Sorted by model distance: nonbonded pdb=" O VAL D 111 " pdb=" OG1 THR D 114 " model vdw 1.962 3.040 nonbonded pdb=" O VAL A 111 " pdb=" OG1 THR A 114 " model vdw 1.962 3.040 nonbonded pdb=" O VAL G 111 " pdb=" OG1 THR G 114 " model vdw 1.963 3.040 nonbonded pdb=" O VAL B 111 " pdb=" OG1 THR B 114 " model vdw 1.963 3.040 nonbonded pdb=" O TYR A 347 " pdb=" NH1 ARG A 353 " model vdw 1.985 3.120 ... (remaining 143963 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 'D' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.990 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 33.430 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 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 : 0.008 0.141 16476 Z= 0.507 Angle : 0.789 14.807 22224 Z= 0.440 Chirality : 0.041 0.169 2428 Planarity : 0.005 0.062 2804 Dihedral : 14.627 163.679 5992 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 92.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.57 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: -3.89 (0.15), residues: 1956 helix: -2.41 (0.10), residues: 1448 sheet: None (None), residues: 0 loop : -2.39 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 360 HIS 0.004 0.002 HIS G 96 PHE 0.026 0.002 PHE F 142 TYR 0.024 0.003 TYR G 280 ARG 0.005 0.001 ARG G 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ILE cc_start: 0.8347 (mm) cc_final: 0.8081 (mm) REVERT: A 266 ASP cc_start: 0.7527 (m-30) cc_final: 0.7247 (m-30) REVERT: F 13 PHE cc_start: 0.3397 (m-10) cc_final: 0.2516 (m-80) REVERT: F 73 MET cc_start: 0.5989 (mmm) cc_final: 0.5524 (mmp) REVERT: B 101 LEU cc_start: 0.8987 (mt) cc_final: 0.8777 (mt) REVERT: B 171 ILE cc_start: 0.8231 (mm) cc_final: 0.7965 (mm) REVERT: B 546 MET cc_start: 0.7897 (tpt) cc_final: 0.7679 (tpp) REVERT: C 54 ASN cc_start: 0.7734 (m-40) cc_final: 0.7526 (t0) REVERT: D 171 ILE cc_start: 0.8289 (mm) cc_final: 0.7974 (mm) REVERT: D 266 ASP cc_start: 0.7372 (m-30) cc_final: 0.7074 (m-30) REVERT: E 13 PHE cc_start: 0.3195 (m-10) cc_final: 0.2326 (m-80) REVERT: E 76 LYS cc_start: 0.6609 (mttt) cc_final: 0.6375 (tptt) REVERT: G 171 ILE cc_start: 0.8303 (mm) cc_final: 0.8006 (mm) REVERT: G 546 MET cc_start: 0.8035 (tpt) cc_final: 0.7801 (tpp) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.3337 time to fit residues: 178.3903 Evaluate side-chains 281 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 59 optimal weight: 0.0870 chunk 93 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 177 optimal weight: 6.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 96 HIS B 78 GLN B 96 HIS C 54 ASN D 78 GLN D 96 HIS ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 GLN G 96 HIS H 50 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16476 Z= 0.278 Angle : 0.801 10.443 22224 Z= 0.419 Chirality : 0.044 0.176 2428 Planarity : 0.005 0.051 2804 Dihedral : 8.943 149.584 2216 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.58 % Favored : 96.06 % Rotamer: Outliers : 1.89 % Allowed : 12.83 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.18 (0.18), residues: 1956 helix: -0.36 (0.12), residues: 1548 sheet: None (None), residues: 0 loop : -1.92 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 288 HIS 0.004 0.001 HIS A 324 PHE 0.022 0.002 PHE F 142 TYR 0.019 0.003 TYR G 363 ARG 0.009 0.001 ARG A 581 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 364 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ILE cc_start: 0.8260 (mm) cc_final: 0.8000 (mm) REVERT: A 209 ILE cc_start: 0.9256 (mt) cc_final: 0.8969 (mt) REVERT: A 211 MET cc_start: 0.7184 (tmm) cc_final: 0.6954 (tmm) REVERT: F 76 LYS cc_start: 0.3192 (tptt) cc_final: 0.2590 (tptt) REVERT: F 126 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.6168 (mm) REVERT: B 171 ILE cc_start: 0.8190 (mm) cc_final: 0.7893 (mm) REVERT: B 176 LEU cc_start: 0.3796 (OUTLIER) cc_final: 0.3582 (mt) REVERT: B 211 MET cc_start: 0.7292 (tmm) cc_final: 0.7023 (tmm) REVERT: C 13 PHE cc_start: 0.2699 (m-10) cc_final: 0.2296 (m-10) REVERT: D 171 ILE cc_start: 0.8244 (mm) cc_final: 0.7957 (mm) REVERT: D 209 ILE cc_start: 0.9230 (mt) cc_final: 0.9001 (mt) REVERT: E 52 MET cc_start: 0.7482 (tmm) cc_final: 0.7101 (tmm) REVERT: E 126 ILE cc_start: 0.6923 (mm) cc_final: 0.6560 (mm) REVERT: G 171 ILE cc_start: 0.8274 (mm) cc_final: 0.8015 (mm) REVERT: G 209 ILE cc_start: 0.9310 (mt) cc_final: 0.9072 (mt) REVERT: H 52 MET cc_start: 0.7780 (tmm) cc_final: 0.7326 (tmm) REVERT: H 77 MET cc_start: 0.0918 (ptm) cc_final: 0.0614 (ptm) REVERT: H 126 ILE cc_start: 0.6738 (mm) cc_final: 0.6337 (mm) outliers start: 32 outliers final: 11 residues processed: 376 average time/residue: 0.2987 time to fit residues: 160.2308 Evaluate side-chains 308 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 295 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 360 TRP Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 250 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 178 optimal weight: 30.0000 chunk 192 optimal weight: 5.9990 chunk 158 optimal weight: 40.0000 chunk 176 optimal weight: 4.9990 chunk 60 optimal weight: 30.0000 chunk 143 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 16476 Z= 0.441 Angle : 0.855 12.573 22224 Z= 0.454 Chirality : 0.048 0.179 2428 Planarity : 0.005 0.051 2804 Dihedral : 9.026 147.942 2216 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 26.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.07 % Allowed : 17.38 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.24 (0.18), residues: 1956 helix: -0.46 (0.12), residues: 1516 sheet: None (None), residues: 0 loop : -1.61 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 288 HIS 0.007 0.001 HIS A 575 PHE 0.023 0.003 PHE A 240 TYR 0.041 0.004 TYR A 363 ARG 0.008 0.001 ARG D 581 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 302 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ILE cc_start: 0.8253 (mm) cc_final: 0.7982 (mm) REVERT: F 76 LYS cc_start: 0.3683 (tptt) cc_final: 0.3068 (tptt) REVERT: F 126 ILE cc_start: 0.6936 (mm) cc_final: 0.6571 (mm) REVERT: B 171 ILE cc_start: 0.8060 (mm) cc_final: 0.7818 (mm) REVERT: B 344 TRP cc_start: 0.5962 (t-100) cc_final: 0.5672 (t-100) REVERT: C 125 MET cc_start: 0.5384 (tmm) cc_final: 0.4977 (ptm) REVERT: D 171 ILE cc_start: 0.8268 (mm) cc_final: 0.8026 (mm) REVERT: E 73 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.6482 (mmm) REVERT: E 76 LYS cc_start: 0.7236 (mttt) cc_final: 0.6971 (tptt) REVERT: E 101 ILE cc_start: 0.3948 (OUTLIER) cc_final: 0.3737 (tt) REVERT: E 126 ILE cc_start: 0.6889 (mm) cc_final: 0.6420 (mm) REVERT: G 171 ILE cc_start: 0.8226 (mm) cc_final: 0.8002 (mm) REVERT: H 126 ILE cc_start: 0.7037 (mm) cc_final: 0.6652 (mm) outliers start: 52 outliers final: 31 residues processed: 326 average time/residue: 0.3087 time to fit residues: 145.6633 Evaluate side-chains 303 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 270 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 546 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 6.9990 chunk 189 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 228 HIS ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 HIS H 9 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16476 Z= 0.263 Angle : 0.738 9.635 22224 Z= 0.389 Chirality : 0.042 0.170 2428 Planarity : 0.005 0.053 2804 Dihedral : 9.064 154.493 2216 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.84 % Allowed : 17.85 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.71 (0.18), residues: 1956 helix: -0.08 (0.12), residues: 1560 sheet: None (None), residues: 0 loop : -1.55 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 288 HIS 0.005 0.001 HIS B 228 PHE 0.028 0.002 PHE D 346 TYR 0.026 0.002 TYR A 363 ARG 0.006 0.001 ARG D 581 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 328 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.7670 (tpp) cc_final: 0.7456 (tpp) REVERT: F 76 LYS cc_start: 0.3840 (tptt) cc_final: 0.3410 (tmtt) REVERT: F 126 ILE cc_start: 0.6720 (mm) cc_final: 0.6372 (mm) REVERT: B 171 ILE cc_start: 0.8012 (mm) cc_final: 0.7788 (mm) REVERT: B 176 LEU cc_start: 0.3478 (OUTLIER) cc_final: 0.3264 (mt) REVERT: C 146 MET cc_start: 0.4835 (mmm) cc_final: 0.4518 (mmm) REVERT: D 130 GLU cc_start: 0.6800 (pt0) cc_final: 0.6347 (pp20) REVERT: D 171 ILE cc_start: 0.8274 (mm) cc_final: 0.7878 (mm) REVERT: D 592 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7666 (mm) REVERT: E 75 ARG cc_start: 0.8053 (mmp80) cc_final: 0.7585 (mmp80) REVERT: E 126 ILE cc_start: 0.6901 (mm) cc_final: 0.6507 (mm) REVERT: G 171 ILE cc_start: 0.8237 (mm) cc_final: 0.7719 (mm) REVERT: H 73 MET cc_start: 0.6625 (mtt) cc_final: 0.6328 (mmm) REVERT: H 125 MET cc_start: 0.5250 (tmm) cc_final: 0.4578 (ptm) REVERT: H 126 ILE cc_start: 0.6929 (mm) cc_final: 0.6118 (mm) outliers start: 48 outliers final: 26 residues processed: 354 average time/residue: 0.3200 time to fit residues: 159.7778 Evaluate side-chains 315 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 287 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain G residue 292 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16476 Z= 0.283 Angle : 0.757 9.001 22224 Z= 0.397 Chirality : 0.042 0.180 2428 Planarity : 0.005 0.058 2804 Dihedral : 9.027 156.472 2216 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.07 % Allowed : 19.86 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.54 (0.18), residues: 1956 helix: -0.02 (0.12), residues: 1584 sheet: None (None), residues: 0 loop : -1.28 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 344 HIS 0.007 0.001 HIS A 575 PHE 0.023 0.002 PHE H 93 TYR 0.022 0.002 TYR A 363 ARG 0.008 0.001 ARG G 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 317 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.6959 (pt0) cc_final: 0.6520 (pp20) REVERT: A 546 MET cc_start: 0.7805 (tpp) cc_final: 0.7498 (tpp) REVERT: F 126 ILE cc_start: 0.6844 (mm) cc_final: 0.6359 (mm) REVERT: B 130 GLU cc_start: 0.7091 (pt0) cc_final: 0.6517 (pp20) REVERT: B 137 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: B 171 ILE cc_start: 0.8072 (mm) cc_final: 0.7835 (mm) REVERT: C 125 MET cc_start: 0.5466 (tmm) cc_final: 0.5055 (ppp) REVERT: D 171 ILE cc_start: 0.8033 (mm) cc_final: 0.7819 (mm) REVERT: E 37 MET cc_start: 0.6363 (mpp) cc_final: 0.6106 (ptp) REVERT: E 73 MET cc_start: 0.6729 (mtt) cc_final: 0.6437 (mmm) REVERT: E 75 ARG cc_start: 0.8012 (mmp80) cc_final: 0.7635 (mmp80) REVERT: E 76 LYS cc_start: 0.7211 (mttt) cc_final: 0.6882 (tptt) REVERT: E 101 ILE cc_start: 0.3606 (OUTLIER) cc_final: 0.3390 (tp) REVERT: E 125 MET cc_start: 0.5300 (tmm) cc_final: 0.4658 (ptm) REVERT: E 126 ILE cc_start: 0.7203 (mm) cc_final: 0.6231 (mm) REVERT: E 127 ARG cc_start: 0.7297 (tpt90) cc_final: 0.6617 (mmm160) REVERT: G 130 GLU cc_start: 0.6876 (pt0) cc_final: 0.6406 (pp20) REVERT: G 171 ILE cc_start: 0.8026 (mm) cc_final: 0.7776 (mm) REVERT: H 73 MET cc_start: 0.6742 (mtt) cc_final: 0.6358 (mmm) REVERT: H 126 ILE cc_start: 0.7100 (mm) cc_final: 0.6602 (mm) outliers start: 52 outliers final: 29 residues processed: 350 average time/residue: 0.3282 time to fit residues: 163.4104 Evaluate side-chains 322 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 291 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 137 PHE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 292 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 189 optimal weight: 0.0170 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 HIS ** G 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.6395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16476 Z= 0.234 Angle : 0.754 9.856 22224 Z= 0.388 Chirality : 0.041 0.242 2428 Planarity : 0.005 0.067 2804 Dihedral : 8.955 159.214 2216 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.78 % Allowed : 20.98 % 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: -0.16 (0.19), residues: 1956 helix: 0.21 (0.12), residues: 1572 sheet: None (None), residues: 0 loop : -0.96 (0.36), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 344 HIS 0.007 0.001 HIS B 575 PHE 0.025 0.002 PHE E 142 TYR 0.019 0.002 TYR A 363 ARG 0.009 0.001 ARG B 581 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 325 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.6822 (pt0) cc_final: 0.6461 (pp20) REVERT: A 546 MET cc_start: 0.7802 (tpp) cc_final: 0.7327 (tpp) REVERT: F 73 MET cc_start: 0.6799 (mmm) cc_final: 0.6392 (mmm) REVERT: F 101 ILE cc_start: 0.3504 (OUTLIER) cc_final: 0.3303 (tp) REVERT: F 126 ILE cc_start: 0.6724 (mm) cc_final: 0.6448 (mm) REVERT: B 130 GLU cc_start: 0.7000 (pt0) cc_final: 0.6460 (pp20) REVERT: C 73 MET cc_start: 0.6871 (mmm) cc_final: 0.6524 (mmm) REVERT: C 125 MET cc_start: 0.5462 (tmm) cc_final: 0.5112 (ppp) REVERT: D 592 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7723 (mm) REVERT: E 75 ARG cc_start: 0.8138 (mmp80) cc_final: 0.7752 (mmp80) REVERT: E 76 LYS cc_start: 0.7319 (mttt) cc_final: 0.7086 (tptt) REVERT: E 125 MET cc_start: 0.5545 (tmm) cc_final: 0.5093 (ptm) REVERT: E 126 ILE cc_start: 0.7081 (mm) cc_final: 0.6024 (mm) REVERT: E 127 ARG cc_start: 0.7242 (tpt90) cc_final: 0.6542 (mmm160) REVERT: G 130 GLU cc_start: 0.6797 (pt0) cc_final: 0.6383 (pp20) REVERT: H 125 MET cc_start: 0.5298 (tmm) cc_final: 0.4633 (ptm) REVERT: H 126 ILE cc_start: 0.7087 (mm) cc_final: 0.6280 (mm) outliers start: 47 outliers final: 31 residues processed: 352 average time/residue: 0.3179 time to fit residues: 156.6810 Evaluate side-chains 322 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 289 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 324 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 138 optimal weight: 0.0070 chunk 107 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 188 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 586 GLN ** G 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.6819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16476 Z= 0.218 Angle : 0.765 10.867 22224 Z= 0.391 Chirality : 0.041 0.216 2428 Planarity : 0.004 0.047 2804 Dihedral : 8.923 160.343 2216 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.66 % Allowed : 21.39 % Favored : 75.95 % 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: 0.04 (0.19), residues: 1956 helix: 0.33 (0.12), residues: 1576 sheet: None (None), residues: 0 loop : -0.78 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 344 HIS 0.021 0.001 HIS B 96 PHE 0.029 0.002 PHE E 142 TYR 0.018 0.002 TYR A 363 ARG 0.007 0.001 ARG H 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 329 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.6956 (pt0) cc_final: 0.6486 (pp20) REVERT: A 546 MET cc_start: 0.7750 (tpp) cc_final: 0.7218 (tpp) REVERT: F 126 ILE cc_start: 0.6702 (mm) cc_final: 0.6383 (mm) REVERT: B 130 GLU cc_start: 0.6915 (pt0) cc_final: 0.6503 (pp20) REVERT: B 146 TRP cc_start: 0.7071 (t-100) cc_final: 0.6740 (t60) REVERT: C 13 PHE cc_start: 0.1819 (m-10) cc_final: 0.1323 (m-10) REVERT: C 125 MET cc_start: 0.5695 (tmm) cc_final: 0.5022 (ptm) REVERT: D 130 GLU cc_start: 0.6859 (pt0) cc_final: 0.6349 (pp20) REVERT: D 592 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7714 (mm) REVERT: E 75 ARG cc_start: 0.8157 (mmp80) cc_final: 0.7830 (mmp80) REVERT: E 76 LYS cc_start: 0.7278 (mttt) cc_final: 0.7054 (tmtt) REVERT: E 125 MET cc_start: 0.5733 (tmm) cc_final: 0.5380 (ptm) REVERT: E 126 ILE cc_start: 0.7003 (mm) cc_final: 0.6069 (mm) REVERT: E 146 MET cc_start: 0.5019 (mmm) cc_final: 0.4794 (mmm) REVERT: G 130 GLU cc_start: 0.6749 (pt0) cc_final: 0.6371 (pp20) REVERT: H 73 MET cc_start: 0.6183 (mtt) cc_final: 0.5907 (mtt) REVERT: H 76 LYS cc_start: 0.3698 (tptt) cc_final: 0.3395 (tmtt) REVERT: H 125 MET cc_start: 0.5364 (tmm) cc_final: 0.4851 (ptm) REVERT: H 126 ILE cc_start: 0.6979 (mm) cc_final: 0.6203 (mm) outliers start: 45 outliers final: 31 residues processed: 360 average time/residue: 0.3180 time to fit residues: 161.0476 Evaluate side-chains 323 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 291 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 212 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 324 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 93 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.7168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16476 Z= 0.222 Angle : 0.791 16.287 22224 Z= 0.404 Chirality : 0.042 0.193 2428 Planarity : 0.005 0.070 2804 Dihedral : 8.919 160.956 2216 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.54 % Allowed : 21.81 % Favored : 75.65 % 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: 0.09 (0.19), residues: 1956 helix: 0.37 (0.13), residues: 1576 sheet: None (None), residues: 0 loop : -0.76 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 344 HIS 0.019 0.001 HIS B 96 PHE 0.024 0.002 PHE E 93 TYR 0.016 0.002 TYR A 363 ARG 0.011 0.001 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 316 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.6944 (pt0) cc_final: 0.6455 (pp20) REVERT: F 76 LYS cc_start: 0.4408 (tptt) cc_final: 0.4064 (tptt) REVERT: F 126 ILE cc_start: 0.6670 (mm) cc_final: 0.6354 (mm) REVERT: B 130 GLU cc_start: 0.6873 (pt0) cc_final: 0.6493 (pp20) REVERT: B 146 TRP cc_start: 0.6983 (t-100) cc_final: 0.6632 (t60) REVERT: C 13 PHE cc_start: 0.1842 (m-10) cc_final: 0.1493 (m-10) REVERT: C 125 MET cc_start: 0.5837 (tmm) cc_final: 0.5206 (ptm) REVERT: C 127 ARG cc_start: 0.6976 (mmp80) cc_final: 0.6749 (mmm160) REVERT: D 127 TYR cc_start: 0.5607 (t80) cc_final: 0.5325 (t80) REVERT: D 130 GLU cc_start: 0.6794 (pt0) cc_final: 0.6144 (pp20) REVERT: E 75 ARG cc_start: 0.8099 (mmp80) cc_final: 0.7847 (mmp80) REVERT: E 76 LYS cc_start: 0.7263 (mttt) cc_final: 0.7063 (tmtt) REVERT: E 125 MET cc_start: 0.5937 (tmm) cc_final: 0.5488 (ptm) REVERT: E 126 ILE cc_start: 0.6842 (mm) cc_final: 0.5922 (mm) REVERT: E 127 ARG cc_start: 0.6729 (tpt90) cc_final: 0.6167 (mmm160) REVERT: G 130 GLU cc_start: 0.6726 (pt0) cc_final: 0.6287 (pp20) REVERT: H 76 LYS cc_start: 0.3692 (tptt) cc_final: 0.3476 (tmtt) REVERT: H 125 MET cc_start: 0.5291 (tmm) cc_final: 0.4626 (ptm) REVERT: H 126 ILE cc_start: 0.6940 (mm) cc_final: 0.6193 (mm) outliers start: 43 outliers final: 32 residues processed: 344 average time/residue: 0.3238 time to fit residues: 159.3849 Evaluate side-chains 332 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 300 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 324 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 7.9990 chunk 180 optimal weight: 0.5980 chunk 165 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 138 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16476 Z= 0.274 Angle : 0.814 10.782 22224 Z= 0.422 Chirality : 0.045 0.219 2428 Planarity : 0.005 0.082 2804 Dihedral : 8.926 160.151 2216 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.60 % Allowed : 22.22 % Favored : 75.18 % 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: -0.08 (0.19), residues: 1956 helix: 0.24 (0.12), residues: 1580 sheet: None (None), residues: 0 loop : -0.77 (0.37), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 344 HIS 0.020 0.002 HIS G 96 PHE 0.025 0.002 PHE F 93 TYR 0.019 0.002 TYR G 237 ARG 0.016 0.001 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 298 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.6970 (pt0) cc_final: 0.6321 (pp20) REVERT: F 13 PHE cc_start: 0.1950 (m-10) cc_final: 0.1159 (m-10) REVERT: F 126 ILE cc_start: 0.6867 (mm) cc_final: 0.6622 (mm) REVERT: F 146 MET cc_start: 0.3865 (mmt) cc_final: 0.2893 (mmm) REVERT: B 130 GLU cc_start: 0.6979 (pt0) cc_final: 0.6476 (pp20) REVERT: B 146 TRP cc_start: 0.7114 (t-100) cc_final: 0.6750 (t60) REVERT: B 547 ARG cc_start: 0.8515 (mmt90) cc_final: 0.8242 (mmt90) REVERT: C 125 MET cc_start: 0.6008 (tmm) cc_final: 0.5465 (ptm) REVERT: D 127 TYR cc_start: 0.5778 (t80) cc_final: 0.5464 (t80) REVERT: D 130 GLU cc_start: 0.6885 (pt0) cc_final: 0.6137 (pp20) REVERT: E 75 ARG cc_start: 0.8112 (mmp80) cc_final: 0.7843 (mmp80) REVERT: E 76 LYS cc_start: 0.7289 (mttt) cc_final: 0.7035 (tmtt) REVERT: E 125 MET cc_start: 0.5932 (tmm) cc_final: 0.5360 (ptt) REVERT: E 126 ILE cc_start: 0.6848 (mm) cc_final: 0.6051 (mm) REVERT: G 130 GLU cc_start: 0.6772 (pt0) cc_final: 0.6255 (pp20) REVERT: H 76 LYS cc_start: 0.3882 (tptt) cc_final: 0.3607 (tmtt) REVERT: H 125 MET cc_start: 0.5381 (tmm) cc_final: 0.4755 (ptm) REVERT: H 126 ILE cc_start: 0.6980 (mm) cc_final: 0.6192 (mm) outliers start: 44 outliers final: 39 residues processed: 324 average time/residue: 0.3190 time to fit residues: 146.5289 Evaluate side-chains 331 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 292 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 CYS Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 324 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.5980 chunk 186 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 195 optimal weight: 8.9990 chunk 179 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.7555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16476 Z= 0.222 Angle : 0.832 11.072 22224 Z= 0.427 Chirality : 0.045 0.280 2428 Planarity : 0.005 0.079 2804 Dihedral : 9.015 163.344 2216 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.89 % Allowed : 23.17 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.13 (0.19), residues: 1956 helix: 0.37 (0.13), residues: 1584 sheet: None (None), residues: 0 loop : -0.63 (0.36), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 344 HIS 0.021 0.001 HIS G 96 PHE 0.038 0.002 PHE C 13 TYR 0.019 0.001 TYR G 237 ARG 0.018 0.001 ARG G 541 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 310 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.6890 (pt0) cc_final: 0.6381 (pp20) REVERT: F 126 ILE cc_start: 0.6547 (mm) cc_final: 0.6330 (mm) REVERT: B 130 GLU cc_start: 0.6867 (pt0) cc_final: 0.6474 (pp20) REVERT: B 146 TRP cc_start: 0.6745 (t-100) cc_final: 0.6462 (t60) REVERT: B 547 ARG cc_start: 0.8524 (mmt90) cc_final: 0.8225 (mmt90) REVERT: C 110 MET cc_start: 0.6264 (ppp) cc_final: 0.6002 (ppp) REVERT: C 125 MET cc_start: 0.5877 (tmm) cc_final: 0.5335 (ptm) REVERT: D 130 GLU cc_start: 0.6761 (pt0) cc_final: 0.6121 (pp20) REVERT: E 76 LYS cc_start: 0.7346 (mttt) cc_final: 0.7106 (tmtt) REVERT: E 125 MET cc_start: 0.5990 (tmm) cc_final: 0.5512 (ptm) REVERT: E 126 ILE cc_start: 0.6778 (mm) cc_final: 0.5897 (mm) REVERT: E 127 ARG cc_start: 0.6704 (tpt90) cc_final: 0.6040 (mmm160) REVERT: H 38 ARG cc_start: 0.7386 (mmm160) cc_final: 0.6779 (tpt90) REVERT: H 125 MET cc_start: 0.5058 (tmm) cc_final: 0.4452 (ptm) REVERT: H 126 ILE cc_start: 0.6986 (mm) cc_final: 0.6232 (mm) outliers start: 32 outliers final: 24 residues processed: 330 average time/residue: 0.3167 time to fit residues: 147.9756 Evaluate side-chains 309 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 285 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 324 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 47 optimal weight: 0.0970 chunk 143 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.177200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.142783 restraints weight = 48218.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.140447 restraints weight = 29130.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.141308 restraints weight = 18927.025| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.7784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16476 Z= 0.217 Angle : 0.839 13.491 22224 Z= 0.428 Chirality : 0.044 0.278 2428 Planarity : 0.005 0.112 2804 Dihedral : 9.054 163.977 2216 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.77 % Allowed : 23.82 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.13 (0.19), residues: 1956 helix: 0.35 (0.13), residues: 1596 sheet: None (None), residues: 0 loop : -0.53 (0.37), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 344 HIS 0.020 0.001 HIS G 96 PHE 0.023 0.002 PHE G 346 TYR 0.020 0.001 TYR G 237 ARG 0.021 0.001 ARG D 213 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3428.01 seconds wall clock time: 62 minutes 21.77 seconds (3741.77 seconds total)