Starting phenix.real_space_refine on Wed Oct 9 14:18:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve6_43166/10_2024/8ve6_43166.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve6_43166/10_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_43166/10_2024/8ve6_43166.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve6_43166/10_2024/8ve6_43166.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve6_43166/10_2024/8ve6_43166.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve6_43166/10_2024/8ve6_43166.cif" } 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. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 2.89, per 1000 atoms: 0.91 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 487.6 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... Secondary structure from input PDB file: 4 helices and 5 sheets defined 7.1% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 74 through 82 removed outlier: 3.617A pdb=" N ALA A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 82 " --> pdb=" O TYR A 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 81 removed outlier: 3.658A pdb=" N ALA B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 82 removed outlier: 3.590A pdb=" N TRP C 79 " --> pdb=" O THR C 75 " (cutoff:3.500A) 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) removed outlier: 3.667A pdb=" N LEU C 82 " --> pdb=" O TYR C 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 75 through 82' Processing helix chain 'D' and resid 75 through 83 removed outlier: 3.563A pdb=" N LYS D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 6.505A pdb=" N LEU A 17 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 106 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 removed outlier: 6.505A pdb=" N LEU A 17 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N MET B 13 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA B 109 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS B 15 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU B 111 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU B 17 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 48 removed outlier: 5.841A pdb=" N ARG A 34 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS A 70 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 95 " --> pdb=" O TYR A 69 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N HIS A 88 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE B 95 " --> pdb=" O HIS A 88 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N HIS A 90 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 93 " --> pdb=" O HIS A 90 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N GLU A 92 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA B 91 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL A 94 " --> pdb=" O GLU B 89 " (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) Processing sheet with id=AA4, first strand: chain 'C' and resid 23 through 24 removed outlier: 3.535A pdb=" N SER C 23 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR C 119 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N MET D 13 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ALA D 109 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS D 15 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU D 111 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU D 17 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 47 removed outlier: 3.622A pdb=" N GLU C 42 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 32 " --> pdb=" O PHE C 44 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER C 46 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL C 30 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 70 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE C 95 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 93 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 91 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N HIS C 88 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE D 95 " --> pdb=" O HIS C 88 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N HIS C 90 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL D 93 " --> pdb=" O HIS C 90 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLU C 92 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA D 91 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL C 94 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY D 67 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS D 70 " --> pdb=" O PHE D 33 " (cutoff:3.500A) 113 hydrogen bonds defined for protein. 294 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: 0.82 Time building geometry restraints manager: 0.99 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: 0.00 - 3.13: 4473 3.13 - 6.26: 28 6.26 - 9.39: 2 9.39 - 12.52: 1 12.52 - 15.65: 1 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: 548 2.76 - 3.30: 2892 3.30 - 3.83: 5000 3.83 - 4.37: 5466 4.37 - 4.90: 9848 Nonbonded interactions: 23754 Sorted by model distance: nonbonded pdb=" OH TYR A 116 " pdb=" OH TYR B 116 " model vdw 2.230 3.040 nonbonded pdb=" O VAL A 65 " pdb=" OH TYR A 69 " model vdw 2.232 3.040 nonbonded pdb=" NH1 ARG A 103 " pdb=" O THR A 123 " model vdw 2.238 3.120 nonbonded pdb=" NZ LYS B 35 " pdb=" O ALA B 36 " model vdw 2.303 3.120 nonbonded pdb=" O PRO A 102 " pdb=" NE ARG A 103 " model vdw 2.336 3.120 ... (remaining 23749 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 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: 0.770 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.070 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.050 ------------------------------------------------------------------------------- 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= 0.281 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 : 0.372 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: 0.1612 time to fit residues: 13.8382 Evaluate side-chains 57 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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: 20.0000 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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: 0.8122 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3272 Z= 0.235 Angle : 0.602 7.212 4505 Z= 0.304 Chirality : 0.048 0.140 518 Planarity : 0.005 0.055 584 Dihedral : 7.219 81.676 493 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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: -0.13 (0.41), residues: 457 helix: -0.45 (1.09), residues: 22 sheet: 0.46 (0.39), residues: 194 loop : -0.46 (0.43), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 79 HIS 0.005 0.001 HIS B 88 PHE 0.009 0.001 PHE B 44 TYR 0.016 0.001 TYR C 116 ARG 0.002 0.000 ARG A 34 *********************** 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 71 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.380 Fit side-chains REVERT: B 93 VAL cc_start: 0.9692 (t) cc_final: 0.9458 (m) REVERT: D 13 MET cc_start: 0.8301 (tmm) cc_final: 0.7389 (tpp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1215 time to fit residues: 10.9663 Evaluate side-chains 61 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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: 0.4980 chunk 12 optimal weight: 0.0980 chunk 33 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 11 optimal weight: 0.1980 chunk 40 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.8027 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3272 Z= 0.130 Angle : 0.545 6.276 4505 Z= 0.270 Chirality : 0.047 0.141 518 Planarity : 0.005 0.047 584 Dihedral : 6.765 78.728 493 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: -0.06 (0.41), residues: 457 helix: -0.21 (0.95), residues: 28 sheet: 0.60 (0.38), residues: 195 loop : -0.53 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 79 HIS 0.004 0.001 HIS A 90 PHE 0.009 0.001 PHE C 87 TYR 0.015 0.001 TYR C 116 ARG 0.002 0.000 ARG A 34 *********************** 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 75 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: B 93 VAL cc_start: 0.9666 (t) cc_final: 0.9437 (m) REVERT: D 13 MET cc_start: 0.8257 (tmm) cc_final: 0.7406 (tpp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1256 time to fit residues: 12.0473 Evaluate side-chains 64 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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: 10.0000 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.8098 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3272 Z= 0.221 Angle : 0.535 6.265 4505 Z= 0.277 Chirality : 0.047 0.137 518 Planarity : 0.005 0.051 584 Dihedral : 6.876 83.814 493 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.44 % Allowed : 2.22 % 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: -0.02 (0.41), residues: 457 helix: 0.94 (1.21), residues: 23 sheet: 0.52 (0.39), residues: 189 loop : -0.50 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 79 HIS 0.005 0.001 HIS B 88 PHE 0.011 0.001 PHE B 44 TYR 0.015 0.002 TYR C 114 ARG 0.002 0.000 ARG A 34 *********************** 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 76 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.394 Fit side-chains REVERT: A 34 ARG cc_start: 0.8011 (tpt-90) cc_final: 0.7707 (tpt-90) REVERT: D 13 MET cc_start: 0.8279 (tmm) cc_final: 0.7417 (tpp) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.1167 time to fit residues: 11.3148 Evaluate side-chains 66 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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: 4.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 overall best weight: 3.2146 ------------------------------------------------------------------------------- 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: 0.8130 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3272 Z= 0.292 Angle : 0.576 6.238 4505 Z= 0.297 Chirality : 0.047 0.141 518 Planarity : 0.005 0.043 584 Dihedral : 7.536 82.707 493 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: -0.22 (0.42), residues: 457 helix: 0.91 (1.19), residues: 23 sheet: 0.29 (0.38), residues: 189 loop : -0.54 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 79 HIS 0.006 0.001 HIS B 88 PHE 0.009 0.001 PHE D 64 TYR 0.016 0.002 TYR C 114 ARG 0.002 0.000 ARG B 34 *********************** 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 70 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.421 Fit side-chains REVERT: A 15 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8497 (mmtt) REVERT: A 34 ARG cc_start: 0.7990 (tpt-90) cc_final: 0.7671 (tpt-90) REVERT: D 13 MET cc_start: 0.8290 (tmm) cc_final: 0.7418 (tpp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1387 time to fit residues: 12.2099 Evaluate side-chains 59 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8146 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3272 Z= 0.321 Angle : 0.588 6.779 4505 Z= 0.304 Chirality : 0.048 0.140 518 Planarity : 0.005 0.041 584 Dihedral : 7.655 81.399 493 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % 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: -0.35 (0.42), residues: 457 helix: 0.86 (1.19), residues: 23 sheet: 0.23 (0.39), residues: 189 loop : -0.67 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.007 0.002 HIS B 88 PHE 0.010 0.002 PHE B 44 TYR 0.014 0.002 TYR B 78 ARG 0.002 0.001 ARG A 34 *********************** 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 64 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.406 Fit side-chains REVERT: A 15 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8549 (mmtt) REVERT: A 34 ARG cc_start: 0.7986 (tpt-90) cc_final: 0.7611 (tpt-90) REVERT: D 13 MET cc_start: 0.8310 (tmm) cc_final: 0.7430 (tpp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1176 time to fit residues: 9.7820 Evaluate side-chains 54 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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: 6.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 12 optimal weight: 0.3980 chunk 8 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- 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: 0.8133 moved from start: 0.2346 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= 0.283 Angle : 0.565 7.165 4505 Z= 0.291 Chirality : 0.047 0.139 518 Planarity : 0.005 0.045 584 Dihedral : 7.563 83.284 493 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.22 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: -0.41 (0.41), residues: 457 helix: 0.88 (1.26), residues: 22 sheet: 0.15 (0.38), residues: 189 loop : -0.67 (0.43), residues: 246 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 0.007 0.001 PHE B 33 TYR 0.014 0.002 TYR C 116 ARG 0.002 0.000 ARG A 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 : 0.381 Fit side-chains REVERT: A 15 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8519 (mmtt) REVERT: A 34 ARG cc_start: 0.8053 (tpt-90) cc_final: 0.7651 (tpt-90) REVERT: D 13 MET cc_start: 0.8319 (tmm) cc_final: 0.7499 (tpp) REVERT: D 14 VAL cc_start: 0.9325 (p) cc_final: 0.9099 (p) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1422 time to fit residues: 11.9490 Evaluate side-chains 57 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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: 0.5980 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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: 0.8132 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3272 Z= 0.268 Angle : 0.573 7.521 4505 Z= 0.293 Chirality : 0.047 0.139 518 Planarity : 0.005 0.049 584 Dihedral : 7.535 86.243 493 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % 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: -0.40 (0.42), residues: 457 helix: 1.31 (1.50), residues: 16 sheet: 0.11 (0.39), residues: 189 loop : -0.62 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.005 0.001 HIS B 88 PHE 0.012 0.001 PHE B 44 TYR 0.014 0.002 TYR C 116 ARG 0.003 0.000 ARG A 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 65 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.376 Fit side-chains REVERT: A 34 ARG cc_start: 0.8063 (tpt-90) cc_final: 0.7561 (tpt-90) REVERT: D 13 MET cc_start: 0.8329 (tmm) cc_final: 0.7457 (tpp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1144 time to fit residues: 9.6080 Evaluate side-chains 57 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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: 5.9990 chunk 37 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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: 0.8057 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3272 Z= 0.146 Angle : 0.546 7.410 4505 Z= 0.269 Chirality : 0.047 0.131 518 Planarity : 0.005 0.049 584 Dihedral : 7.363 88.212 493 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: -0.20 (0.42), residues: 457 helix: 1.77 (1.61), residues: 16 sheet: 0.24 (0.38), residues: 189 loop : -0.50 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 79 HIS 0.005 0.001 HIS A 90 PHE 0.010 0.001 PHE B 33 TYR 0.014 0.001 TYR C 116 ARG 0.002 0.000 ARG A 34 *********************** 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 71 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8467 (mmtt) REVERT: A 34 ARG cc_start: 0.8145 (tpt-90) cc_final: 0.7748 (tpt-90) REVERT: B 93 VAL cc_start: 0.9699 (t) cc_final: 0.9438 (m) REVERT: D 13 MET cc_start: 0.8286 (tmm) cc_final: 0.7476 (tpp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1214 time to fit residues: 11.1356 Evaluate side-chains 64 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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: 5.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3272 Z= 0.333 Angle : 0.595 7.871 4505 Z= 0.308 Chirality : 0.048 0.140 518 Planarity : 0.005 0.050 584 Dihedral : 7.498 85.151 493 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % 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: -0.36 (0.42), residues: 457 helix: 1.75 (1.51), residues: 17 sheet: 0.14 (0.39), residues: 187 loop : -0.64 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 79 HIS 0.009 0.002 HIS B 88 PHE 0.010 0.002 PHE B 44 TYR 0.019 0.002 TYR C 114 ARG 0.003 0.001 ARG A 34 ********************** 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 66 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.506 Fit side-chains REVERT: A 15 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8509 (mmtt) REVERT: A 34 ARG cc_start: 0.8110 (tpt-90) cc_final: 0.7596 (tpt-90) REVERT: D 13 MET cc_start: 0.8324 (tmm) cc_final: 0.7489 (tpp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1415 time to fit residues: 12.1128 Evaluate side-chains 58 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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: 0.0070 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 29 optimal weight: 0.2980 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.120815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.093278 restraints weight = 7042.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095673 restraints weight = 4680.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097368 restraints weight = 3619.197| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3272 Z= 0.119 Angle : 0.535 7.464 4505 Z= 0.265 Chirality : 0.046 0.126 518 Planarity : 0.005 0.052 584 Dihedral : 7.256 89.932 493 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: -0.17 (0.41), residues: 457 helix: 1.86 (1.56), residues: 17 sheet: 0.26 (0.38), residues: 190 loop : -0.49 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.005 0.001 HIS A 90 PHE 0.010 0.001 PHE A 87 TYR 0.012 0.001 TYR C 116 ARG 0.002 0.000 ARG A 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1132.55 seconds wall clock time: 22 minutes 24.10 seconds (1344.10 seconds total)