Starting phenix.real_space_refine on Mon Jun 24 14:57:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve6_43166/06_2024/8ve6_43166_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve6_43166/06_2024/8ve6_43166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve6_43166/06_2024/8ve6_43166.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve6_43166/06_2024/8ve6_43166.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve6_43166/06_2024/8ve6_43166_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve6_43166/06_2024/8ve6_43166_updated.pdb" } resolution = 4.1 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= 0.001 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 1 5.16 5 Cl 2 4.86 5 C 2079 2.51 5 N 555 2.21 5 O 541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 18": "OD1" <-> "OD2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3178 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 807 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 789 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 795 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 108} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 766 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 9, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'P2C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.86, per 1000 atoms: 0.90 Number of scatterers: 3178 At special positions: 0 Unit cell: (76.994, 66.316, 65.754, 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) Cl 2 17.00 S 1 16.00 O 541 8.00 N 555 7.00 C 2079 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 - 3.50 Amino acid : False - 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: 1.04 Conformation dependent library (CDL) restraints added in 784.5 milliseconds 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 874 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 4 helices and 8 sheets defined 5.4% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.617A pdb=" N ALA A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.507A pdb=" N LYS C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 81' Processing helix chain 'D' and resid 76 through 82 removed outlier: 3.563A pdb=" N LYS D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 54 through 56 removed outlier: 6.688A pdb=" N TYR A 105 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LYS A 15 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE A 107 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG A 104 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 123 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 106 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 119 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 91 through 96 removed outlier: 3.692A pdb=" N PHE A 95 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS A 70 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG A 34 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 12 through 18 removed outlier: 6.929A pdb=" N TYR B 105 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N LYS B 15 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE B 107 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N LEU B 17 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA B 109 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 90 through 97 removed outlier: 5.606A pdb=" N ILE B 68 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 70 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA B 29 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ARG B 34 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 90 through 93 removed outlier: 3.674A pdb=" N ALA C 91 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 93 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 70 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY C 47 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA C 45 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ARG C 34 " --> pdb=" O PRO C 43 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 106 through 112 removed outlier: 3.636A pdb=" N THR C 119 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 12 through 18 removed outlier: 6.693A pdb=" N TYR D 105 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N LYS D 15 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE D 107 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU D 17 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA D 109 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.789A pdb=" N LYS D 70 " --> pdb=" O PHE D 33 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY D 67 " --> pdb=" O ALA D 97 " (cutoff:3.500A) 88 hydrogen bonds defined for protein. 231 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: 0.73 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1026 1.34 - 1.46: 652 1.46 - 1.57: 1590 1.57 - 1.68: 0 1.68 - 1.80: 4 Bond restraints: 3272 Sorted by residual: bond pdb=" O10 P2C B 201 " pdb=" O11 P2C B 201 " ideal model delta sigma weight residual 1.376 1.472 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C5 P2C B 201 " pdb=" N18 P2C B 201 " ideal model delta sigma weight residual 1.361 1.405 -0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" C13 P2C B 201 " pdb=" C19 P2C B 201 " ideal model delta sigma weight residual 1.527 1.495 0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C2 P2C B 201 " pdb=" C3 P2C B 201 " ideal model delta sigma weight residual 1.393 1.411 -0.018 2.00e-02 2.50e+03 8.15e-01 bond pdb=" C13 P2C B 201 " pdb=" C14 P2C B 201 " ideal model delta sigma weight residual 1.401 1.419 -0.018 2.00e-02 2.50e+03 8.05e-01 ... (remaining 3267 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.19: 139 107.19 - 113.90: 1807 113.90 - 120.61: 1190 120.61 - 127.32: 1320 127.32 - 134.02: 49 Bond angle restraints: 4505 Sorted by residual: angle pdb=" C2 P2C B 201 " pdb=" O9 P2C B 201 " pdb=" O10 P2C B 201 " ideal model delta sigma weight residual 109.84 125.49 -15.65 3.00e+00 1.11e-01 2.72e+01 angle pdb=" O11 P2C B 201 " pdb=" O10 P2C B 201 " pdb=" O9 P2C B 201 " ideal model delta sigma weight residual 108.44 119.83 -11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C ASN C 124 " pdb=" N PRO C 125 " pdb=" CD PRO C 125 " ideal model delta sigma weight residual 125.00 132.65 -7.65 4.10e+00 5.95e-02 3.48e+00 angle pdb=" N GLY C 67 " pdb=" CA GLY C 67 " pdb=" C GLY C 67 " ideal model delta sigma weight residual 111.66 115.08 -3.42 1.91e+00 2.74e-01 3.21e+00 angle pdb=" N THR B 75 " pdb=" CA THR B 75 " pdb=" C THR B 75 " ideal model delta sigma weight residual 113.18 110.84 2.34 1.33e+00 5.65e-01 3.08e+00 ... (remaining 4500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 1711 15.85 - 31.70: 120 31.70 - 47.54: 20 47.54 - 63.39: 2 63.39 - 79.24: 4 Dihedral angle restraints: 1857 sinusoidal: 505 harmonic: 1352 Sorted by residual: dihedral pdb=" CG ARG B 34 " pdb=" CD ARG B 34 " pdb=" NE ARG B 34 " pdb=" CZ ARG B 34 " ideal model delta sinusoidal sigma weight residual 90.00 134.45 -44.45 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA PRO D 86 " pdb=" C PRO D 86 " pdb=" N PHE D 87 " pdb=" CA PHE D 87 " ideal model delta harmonic sigma weight residual 180.00 164.32 15.68 0 5.00e+00 4.00e-02 9.84e+00 dihedral pdb=" CG LYS B 70 " pdb=" CD LYS B 70 " pdb=" CE LYS B 70 " pdb=" NZ LYS B 70 " ideal model delta sinusoidal sigma weight residual 180.00 130.93 49.07 3 1.50e+01 4.44e-03 8.73e+00 ... (remaining 1854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 256 0.026 - 0.051: 148 0.051 - 0.077: 46 0.077 - 0.102: 39 0.102 - 0.128: 29 Chirality restraints: 518 Sorted by residual: chirality pdb=" CA PRO A 113 " pdb=" N PRO A 113 " pdb=" C PRO A 113 " pdb=" CB PRO A 113 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA VAL D 28 " pdb=" N VAL D 28 " pdb=" C VAL D 28 " pdb=" CB VAL D 28 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 515 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 101 " -0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO C 102 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 85 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO D 86 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 86 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 86 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 85 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO B 86 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 86 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 86 " -0.027 5.00e-02 4.00e+02 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 553 2.76 - 3.30: 2905 3.30 - 3.83: 5033 3.83 - 4.37: 5490 4.37 - 4.90: 9857 Nonbonded interactions: 23838 Sorted by model distance: nonbonded pdb=" OH TYR A 116 " pdb=" OH TYR B 116 " model vdw 2.230 2.440 nonbonded pdb=" O VAL A 65 " pdb=" OH TYR A 69 " model vdw 2.232 2.440 nonbonded pdb=" NH1 ARG A 103 " pdb=" O THR A 123 " model vdw 2.238 2.520 nonbonded pdb=" NZ LYS B 35 " pdb=" O ALA B 36 " model vdw 2.303 2.520 nonbonded pdb=" O PRO A 102 " pdb=" NE ARG A 103 " model vdw 2.336 2.520 ... (remaining 23833 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 14 or (resid 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 20 or (resid 21 and (name N or nam \ e CA or name C or name O or name CB )) or resid 22 or (resid 23 and (name N or n \ ame CA or name C or name O or name CB )) or resid 24 through 33 or (resid 34 thr \ ough 40 and (name N or name CA or name C or name O or name CB )) or resid 41 thr \ ough 47 or (resid 48 through 52 and (name N or name CA or name C or name O or na \ me CB )) or (resid 53 through 62 and (name N or name CA or name C or name O or n \ ame CB )) or resid 63 through 68 or (resid 69 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 o \ r name CZ )) or resid 70 through 71 or (resid 72 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 79 or (resid 80 through \ 82 and (name N or name CA or name C or name O or name CB )) or (resid 83 throug \ h 85 and (name N or name CA or name C or name O or name CB )) or resid 86 throug \ h 97 or (resid 98 through 100 and (name N or name CA or name C or name O or name \ CB )) or resid 101 through 102 or (resid 103 through 104 and (name N or name CA \ or name C or name O or name CB )) or resid 105 or (resid 106 and (name N or nam \ e CA or name C or name O or name CB )) or resid 107 through 109 or (resid 110 an \ d (name N or name CA or name C or name O or name CB )) or resid 111 or (resid 11 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 113 through \ 115 or (resid 116 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 117 t \ hrough 121 and (name N or name CA or name C or name O or name CB )) or resid 122 \ through 123)) selection = (chain 'B' and (resid 10 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 27 or (resid 28 through 30 and (na \ me N or name CA or name C or name O or name CB )) or resid 31 through 33 or (res \ id 34 through 40 and (name N or name CA or name C or name O or name CB )) or res \ id 41 through 53 or (resid 54 through 56 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 57 through 62 and (name N or name CA or name C or na \ me O or name CB )) or resid 63 through 71 or (resid 72 through 77 and (name N or \ name CA or name C or name O or name CB )) or resid 78 through 79 or (resid 80 t \ hrough 82 and (name N or name CA or name C or name O or name CB )) or resid 83 t \ hrough 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) \ or resid 95 or (resid 96 through 100 and (name N or name CA or name C or name O \ or name CB )) or resid 101 through 109 or (resid 110 and (name N or name CA or n \ ame C or name O or name CB )) or resid 111 through 115 or (resid 116 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ )) or resid 117 through 123)) selection = (chain 'C' and (resid 10 through 17 or (resid 18 through 19 and (name N or name \ CA or name C or name O or name CB )) or resid 20 through 22 or (resid 23 and (na \ me N or name CA or name C or name O or name CB )) or resid 24 through 27 or (res \ id 28 through 30 and (name N or name CA or name C or name O or name CB )) or res \ id 31 through 33 or (resid 34 through 40 and (name N or name CA or name C or nam \ e O or name CB )) or resid 41 through 47 or (resid 48 through 52 and (name N or \ name CA or name C or name O or name CB )) or (resid 53 through 56 and (name N or \ name CA or name C or name O or name CB )) or (resid 57 through 62 and (name N o \ r name CA or name C or name O or name CB )) or resid 63 through 64 or (resid 65 \ through 66 and (name N or name CA or name C or name O or name CB )) or resid 67 \ through 72 or (resid 73 through 77 and (name N or name CA or name C or name O or \ name CB )) or resid 78 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 97 or (resid 98 through 100 and (na \ me N or name CA or name C or name O or name CB )) or resid 101 through 102 or (r \ esid 103 through 104 and (name N or name CA or name C or name O or name CB )) or \ resid 105 or (resid 106 and (name N or name CA or name C or name O or name CB ) \ ) or resid 107 through 115 or (resid 116 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or nam \ e CZ )) or (resid 117 through 121 and (name N or name CA or name C or name O or \ name CB )) or resid 122 through 123)) selection = (chain 'D' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 20 or (resid 21 and (name N or nam \ e CA or name C or name O or name CB )) or resid 22 through 25 or (resid 26 throu \ gh 30 and (name N or name CA or name C or name O or name CB )) or resid 31 throu \ gh 47 or (resid 48 through 52 and (name N or name CA or name C or name O or name \ CB )) or (resid 53 through 62 and (name N or name CA or name C or name O or nam \ e CB )) or resid 63 through 64 or (resid 65 through 66 and (name N or name CA or \ name C or name O or name CB )) or resid 67 through 68 or (resid 69 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ )) or resid 70 through 74 or (resid 75 through 7 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 78 through 7 \ 9 or (resid 80 through 82 and (name N or name CA or name C or name O or name CB \ )) or resid 83 through 93 or (resid 94 and (name N or name CA or name C or name \ O or name CB )) or resid 95 through 97 or (resid 98 through 100 and (name N or n \ ame CA or name C or name O or name CB )) or resid 101 through 109 or (resid 110 \ and (name N or name CA or name C or name O or name CB )) or resid 111 or (resid \ 112 and (name N or name CA or name C or name O or name CB )) or resid 113 throug \ h 117 or (resid 118 through 121 and (name N or name CA or name C or name O or na \ me CB )) or resid 122 or (resid 123 and (name N or name CA or name C or name O o \ r name CB )))) } 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.360 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.440 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.010 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.004 0.096 3272 Z= 0.299 Angle : 0.673 15.646 4505 Z= 0.329 Chirality : 0.047 0.128 518 Planarity : 0.006 0.070 584 Dihedral : 11.950 79.240 983 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.41), residues: 457 helix: -0.09 (1.10), residues: 19 sheet: 0.42 (0.40), residues: 194 loop : -0.50 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 41 HIS 0.005 0.001 HIS B 88 PHE 0.011 0.001 PHE B 33 TYR 0.011 0.001 TYR A 114 ARG 0.005 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: C 70 LYS cc_start: 0.8358 (tttt) cc_final: 0.8129 (ttmt) REVERT: D 13 MET cc_start: 0.8185 (tmm) cc_final: 0.7334 (tpp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1347 time to fit residues: 11.3843 Evaluate side-chains 57 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3272 Z= 0.313 Angle : 0.615 7.574 4505 Z= 0.314 Chirality : 0.048 0.141 518 Planarity : 0.006 0.056 584 Dihedral : 6.548 76.616 493 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.48 (0.41), residues: 457 helix: -0.27 (1.09), residues: 19 sheet: 0.15 (0.37), residues: 207 loop : -0.69 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 79 HIS 0.008 0.002 HIS B 88 PHE 0.009 0.001 PHE D 44 TYR 0.012 0.002 TYR C 116 ARG 0.004 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: B 93 VAL cc_start: 0.9697 (t) cc_final: 0.9463 (m) REVERT: D 13 MET cc_start: 0.8204 (tmm) cc_final: 0.7389 (tpp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1418 time to fit residues: 11.7458 Evaluate side-chains 61 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3272 Z= 0.166 Angle : 0.529 6.242 4505 Z= 0.268 Chirality : 0.046 0.134 518 Planarity : 0.005 0.047 584 Dihedral : 5.355 61.675 493 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: -0.20 (0.41), residues: 457 helix: -0.17 (1.26), residues: 18 sheet: 0.44 (0.38), residues: 196 loop : -0.57 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 79 HIS 0.003 0.001 HIS A 90 PHE 0.011 0.001 PHE C 87 TYR 0.012 0.001 TYR C 116 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: D 13 MET cc_start: 0.8291 (tmm) cc_final: 0.7550 (tpt) REVERT: D 78 TYR cc_start: 0.8439 (t80) cc_final: 0.8221 (t80) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1245 time to fit residues: 11.6140 Evaluate side-chains 61 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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: 0.8194 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3272 Z= 0.378 Angle : 0.608 6.291 4505 Z= 0.320 Chirality : 0.048 0.140 518 Planarity : 0.006 0.046 584 Dihedral : 5.808 68.751 493 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.65 (0.41), residues: 457 helix: -0.57 (1.15), residues: 18 sheet: 0.15 (0.38), residues: 199 loop : -0.89 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.009 0.002 HIS B 88 PHE 0.010 0.002 PHE B 44 TYR 0.018 0.002 TYR C 114 ARG 0.003 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.348 Fit side-chains REVERT: A 34 ARG cc_start: 0.7822 (tpt-90) cc_final: 0.7523 (tpt-90) REVERT: D 13 MET cc_start: 0.8284 (tmm) cc_final: 0.7414 (tpp) REVERT: D 78 TYR cc_start: 0.8664 (t80) cc_final: 0.8413 (t80) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1452 time to fit residues: 11.1868 Evaluate side-chains 56 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.0770 chunk 8 optimal weight: 10.0000 overall best weight: 1.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3272 Z= 0.167 Angle : 0.537 6.320 4505 Z= 0.267 Chirality : 0.047 0.133 518 Planarity : 0.005 0.042 584 Dihedral : 5.217 68.138 493 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.43 (0.41), residues: 457 helix: 0.12 (1.32), residues: 18 sheet: 0.21 (0.38), residues: 199 loop : -0.69 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.003 0.001 HIS A 90 PHE 0.013 0.001 PHE D 64 TYR 0.010 0.001 TYR D 116 ARG 0.001 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.344 Fit side-chains REVERT: A 34 ARG cc_start: 0.7851 (tpt-90) cc_final: 0.7506 (tpt-90) REVERT: D 13 MET cc_start: 0.8284 (tmm) cc_final: 0.7409 (tpp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1325 time to fit residues: 11.7013 Evaluate side-chains 57 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 0.0570 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 4 optimal weight: 0.0370 chunk 31 optimal weight: 5.9990 overall best weight: 2.6180 ------------------------------------------------------------------------------- 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: 0.8133 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3272 Z= 0.244 Angle : 0.545 6.529 4505 Z= 0.276 Chirality : 0.047 0.137 518 Planarity : 0.005 0.049 584 Dihedral : 5.066 64.381 493 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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 (0.41), residues: 457 helix: 0.13 (1.33), residues: 18 sheet: 0.27 (0.38), residues: 194 loop : -0.78 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 41 HIS 0.007 0.001 HIS C 88 PHE 0.014 0.001 PHE B 44 TYR 0.017 0.002 TYR C 116 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.367 Fit side-chains REVERT: A 34 ARG cc_start: 0.7851 (tpt-90) cc_final: 0.7486 (tpt-90) REVERT: D 13 MET cc_start: 0.8276 (tmm) cc_final: 0.7415 (tpp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1393 time to fit residues: 11.5071 Evaluate side-chains 55 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.0470 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3272 Z= 0.269 Angle : 0.570 6.939 4505 Z= 0.291 Chirality : 0.048 0.140 518 Planarity : 0.005 0.049 584 Dihedral : 5.103 63.025 493 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.49 (0.41), residues: 457 helix: 0.03 (1.34), residues: 18 sheet: 0.21 (0.39), residues: 190 loop : -0.74 (0.42), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.005 0.001 HIS C 88 PHE 0.006 0.001 PHE C 87 TYR 0.016 0.002 TYR C 116 ARG 0.002 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.314 Fit side-chains REVERT: A 34 ARG cc_start: 0.7841 (tpt-90) cc_final: 0.7439 (tpt-90) REVERT: C 78 TYR cc_start: 0.7814 (t80) cc_final: 0.7585 (t80) REVERT: D 13 MET cc_start: 0.8293 (tmm) cc_final: 0.7434 (tpp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1301 time to fit residues: 10.6793 Evaluate side-chains 52 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.0970 chunk 3 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.0170 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 HIS C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3272 Z= 0.124 Angle : 0.525 6.892 4505 Z= 0.257 Chirality : 0.046 0.127 518 Planarity : 0.005 0.052 584 Dihedral : 4.163 47.555 493 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: -0.12 (0.42), residues: 457 helix: 0.17 (1.39), residues: 18 sheet: 0.42 (0.38), residues: 202 loop : -0.48 (0.44), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 41 HIS 0.008 0.001 HIS C 88 PHE 0.017 0.001 PHE B 44 TYR 0.011 0.001 TYR B 78 ARG 0.002 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7887 (tpt-90) cc_final: 0.7561 (tpt170) REVERT: A 68 ILE cc_start: 0.9399 (mm) cc_final: 0.9087 (mt) REVERT: B 44 PHE cc_start: 0.7935 (t80) cc_final: 0.7731 (t80) REVERT: D 13 MET cc_start: 0.8275 (tmm) cc_final: 0.7420 (tpp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1177 time to fit residues: 11.0390 Evaluate side-chains 60 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 HIS C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3272 Z= 0.246 Angle : 0.553 7.299 4505 Z= 0.281 Chirality : 0.047 0.135 518 Planarity : 0.006 0.054 584 Dihedral : 4.593 51.132 493 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -0.22 (0.41), residues: 457 helix: 0.34 (1.38), residues: 18 sheet: 0.43 (0.39), residues: 187 loop : -0.59 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 79 HIS 0.005 0.001 HIS B 88 PHE 0.013 0.002 PHE B 44 TYR 0.020 0.002 TYR C 114 ARG 0.015 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.354 Fit side-chains REVERT: A 34 ARG cc_start: 0.7919 (tpt-90) cc_final: 0.7459 (tpt-90) REVERT: B 44 PHE cc_start: 0.7984 (t80) cc_final: 0.7752 (t80) REVERT: D 13 MET cc_start: 0.8261 (tmm) cc_final: 0.7383 (tpp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1456 time to fit residues: 11.6857 Evaluate side-chains 56 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 30.0000 chunk 21 optimal weight: 0.0970 chunk 27 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3272 Z= 0.192 Angle : 0.546 7.411 4505 Z= 0.275 Chirality : 0.047 0.135 518 Planarity : 0.006 0.050 584 Dihedral : 4.509 49.268 493 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.19 (0.41), residues: 457 helix: 0.23 (1.40), residues: 18 sheet: 0.41 (0.39), residues: 188 loop : -0.53 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 41 HIS 0.005 0.001 HIS B 88 PHE 0.014 0.001 PHE B 44 TYR 0.017 0.002 TYR C 114 ARG 0.010 0.001 ARG A 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 914 Ramachandran restraints generated. 457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.356 Fit side-chains REVERT: A 34 ARG cc_start: 0.7940 (tpt-90) cc_final: 0.7443 (tpt-90) REVERT: B 44 PHE cc_start: 0.7965 (t80) cc_final: 0.7745 (t80) REVERT: D 13 MET cc_start: 0.8284 (tmm) cc_final: 0.7399 (tpp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1309 time to fit residues: 10.1645 Evaluate side-chains 54 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 0.0070 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.114441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.086800 restraints weight = 7322.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.088856 restraints weight = 5063.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.090395 restraints weight = 4014.105| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3272 Z= 0.379 Angle : 0.626 7.920 4505 Z= 0.325 Chirality : 0.049 0.142 518 Planarity : 0.006 0.065 584 Dihedral : 5.362 54.536 493 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -0.75 (0.41), residues: 457 helix: 0.07 (1.36), residues: 18 sheet: -0.01 (0.38), residues: 194 loop : -0.91 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.008 0.002 HIS B 88 PHE 0.009 0.002 PHE B 44 TYR 0.021 0.002 TYR C 114 ARG 0.011 0.001 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1132.22 seconds wall clock time: 20 minutes 44.90 seconds (1244.90 seconds total)