Starting phenix.real_space_refine on Thu Jul 18 20:43:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve0_43160/07_2024/8ve0_43160.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve0_43160/07_2024/8ve0_43160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve0_43160/07_2024/8ve0_43160.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve0_43160/07_2024/8ve0_43160.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve0_43160/07_2024/8ve0_43160.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve0_43160/07_2024/8ve0_43160.cif" } resolution = 3.1 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 7 5.16 5 C 2281 2.51 5 N 588 2.21 5 O 651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 63": "OE1" <-> "OE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ASP 99": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3527 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 863 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 875 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 108} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 878 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 867 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 109} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'1WZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'1WZ:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'1WZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'1WZ:plan-4': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.87, per 1000 atoms: 0.81 Number of scatterers: 3527 At special positions: 0 Unit cell: (77.556, 68.002, 61.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 7 16.00 O 651 8.00 N 588 7.00 C 2281 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 609.7 milliseconds 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 876 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 5 sheets defined 8.4% alpha, 44.8% 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 83 removed outlier: 4.113A pdb=" N TYR A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 83 removed outlier: 4.006A pdb=" N TYR B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 Processing helix chain 'D' and resid 74 through 83 removed outlier: 3.984A pdb=" N TYR D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 82 " --> pdb=" O TYR D 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 3.577A pdb=" N VAL A 14 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.204A pdb=" N MET A 13 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ALA A 109 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS A 15 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU A 111 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A 17 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N MET B 13 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA B 109 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LYS B 15 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU B 111 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 17 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 48 removed outlier: 6.596A pdb=" N VAL A 32 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A 46 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 30 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE A 68 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 67 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL B 94 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA A 91 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N GLU B 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 93 " --> pdb=" O HIS B 90 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N HIS B 90 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE A 95 " --> pdb=" O HIS B 88 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N HIS B 88 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 67 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE B 68 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 30 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER B 46 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 32 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.333A pdb=" N MET C 13 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ALA C 109 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LYS C 15 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU C 111 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 17 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET D 13 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ALA D 109 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS D 15 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU D 111 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU D 17 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL D 14 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 48 removed outlier: 5.657A pdb=" N ARG C 34 " --> pdb=" O PRO C 43 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA C 29 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE C 68 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N HIS C 88 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE D 95 " --> pdb=" O HIS C 88 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N HIS C 90 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL D 93 " --> pdb=" O HIS C 90 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N GLU C 92 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA D 91 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N VAL C 94 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU D 89 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE D 68 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ARG D 34 " --> pdb=" O PRO D 43 " (cutoff:3.500A) 135 hydrogen bonds defined for protein. 375 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: 0.93 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 559 1.31 - 1.44: 1036 1.44 - 1.56: 2017 1.56 - 1.68: 2 1.68 - 1.81: 10 Bond restraints: 3624 Sorted by residual: bond pdb=" CAH 1WZ C 201 " pdb=" CAR 1WZ C 201 " ideal model delta sigma weight residual 1.461 1.570 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" CAH 1WZ B 201 " pdb=" CAR 1WZ B 201 " ideal model delta sigma weight residual 1.461 1.569 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" CAV 1WZ B 201 " pdb=" NAW 1WZ B 201 " ideal model delta sigma weight residual 1.376 1.473 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" CAV 1WZ C 201 " pdb=" NAW 1WZ C 201 " ideal model delta sigma weight residual 1.376 1.472 -0.096 2.00e-02 2.50e+03 2.33e+01 bond pdb=" CAI 1WZ B 201 " pdb=" CAS 1WZ B 201 " ideal model delta sigma weight residual 1.464 1.548 -0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 3619 not shown) Histogram of bond angle deviations from ideal: 100.78 - 107.42: 157 107.42 - 114.06: 2053 114.06 - 120.70: 1435 120.70 - 127.34: 1256 127.34 - 133.98: 56 Bond angle restraints: 4957 Sorted by residual: angle pdb=" CAH 1WZ B 201 " pdb=" CAI 1WZ B 201 " pdb=" CAS 1WZ B 201 " ideal model delta sigma weight residual 126.24 115.98 10.26 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CAH 1WZ C 201 " pdb=" CAI 1WZ C 201 " pdb=" CAS 1WZ C 201 " ideal model delta sigma weight residual 126.24 116.06 10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" CA LYS C 15 " pdb=" CB LYS C 15 " pdb=" CG LYS C 15 " ideal model delta sigma weight residual 114.10 108.33 5.77 2.00e+00 2.50e-01 8.32e+00 angle pdb=" CB LYS C 80 " pdb=" CG LYS C 80 " pdb=" CD LYS C 80 " ideal model delta sigma weight residual 111.30 117.06 -5.76 2.30e+00 1.89e-01 6.27e+00 angle pdb=" N GLY C 67 " pdb=" CA GLY C 67 " pdb=" C GLY C 67 " ideal model delta sigma weight residual 110.29 113.46 -3.17 1.28e+00 6.10e-01 6.12e+00 ... (remaining 4952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 1914 16.46 - 32.92: 135 32.92 - 49.38: 32 49.38 - 65.84: 8 65.84 - 82.30: 6 Dihedral angle restraints: 2095 sinusoidal: 737 harmonic: 1358 Sorted by residual: dihedral pdb=" CA LYS B 15 " pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " pdb=" CD LYS B 15 " ideal model delta sinusoidal sigma weight residual -180.00 -126.43 -53.57 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N LYS C 15 " pdb=" CA LYS C 15 " pdb=" CB LYS C 15 " pdb=" CG LYS C 15 " ideal model delta sinusoidal sigma weight residual -180.00 -129.56 -50.44 3 1.50e+01 4.44e-03 8.90e+00 dihedral pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " pdb=" CD LYS B 15 " pdb=" CE LYS B 15 " ideal model delta sinusoidal sigma weight residual 60.00 10.16 49.84 3 1.50e+01 4.44e-03 8.83e+00 ... (remaining 2092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 331 0.026 - 0.052: 126 0.052 - 0.078: 39 0.078 - 0.104: 32 0.104 - 0.130: 37 Chirality restraints: 565 Sorted by residual: chirality pdb=" CA ILE A 73 " pdb=" N ILE A 73 " pdb=" C ILE A 73 " pdb=" CB ILE A 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE C 73 " pdb=" N ILE C 73 " pdb=" C ILE C 73 " pdb=" CB ILE C 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE B 73 " pdb=" N ILE B 73 " pdb=" C ILE B 73 " pdb=" CB ILE B 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 562 not shown) Planarity restraints: 627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 112 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO D 113 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 113 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 113 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 112 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO B 113 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 23 " 0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO C 24 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 24 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 24 " 0.015 5.00e-02 4.00e+02 ... (remaining 624 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 552 2.77 - 3.30: 3069 3.30 - 3.83: 5878 3.83 - 4.37: 6612 4.37 - 4.90: 12422 Nonbonded interactions: 28533 Sorted by model distance: nonbonded pdb=" OD2 ASP A 74 " pdb=" OG SER A 77 " model vdw 2.234 2.440 nonbonded pdb=" O VAL B 65 " pdb=" OH TYR B 69 " model vdw 2.238 2.440 nonbonded pdb=" OD2 ASP D 18 " pdb=" OH TYR D 78 " model vdw 2.256 2.440 nonbonded pdb=" OG SER A 117 " pdb=" OAG 1WZ C 201 " model vdw 2.310 2.440 nonbonded pdb=" OE2 GLU C 89 " pdb=" OG1 THR D 96 " model vdw 2.329 2.440 ... (remaining 28528 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 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 45 or (resid 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 62 or (resid 63 and ( \ name N or name CA or name C or name O or name CB )) or resid 64 or (resid 65 thr \ ough 66 and (name N or name CA or name C or name O or name CB )) or resid 67 thr \ ough 76 or (resid 77 and (name N or name CA or name C or name O or name CB )) or \ resid 78 through 91 or (resid 92 and (name N or name CA or name C or name O or \ name CB )) or resid 93 through 95 or (resid 96 through 97 and (name N or name CA \ or name C or name O or name CB )) or resid 98 through 103 or (resid 104 and (na \ me N or name CA or name C or name O or name CB )) or resid 105 through 122 or (r \ esid 123 and (name N or name CA or name C or name O or name CB )) or resid 124)) \ selection = (chain 'B' and (resid 10 through 25 or (resid 26 through 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 through 37 or (resid 38 through \ 40 and (name N or name CA or name C or name O or name CB )) or resid 41 or (res \ id 42 and (name N or name CA or name C or name O or name CB )) or resid 43 throu \ gh 45 or (resid 46 and (name N or name CA or name C or name O or name CB )) or r \ esid 47 through 50 or (resid 51 and (name N or name CA or name C or name O or na \ me CB )) or resid 52 through 58 or (resid 59 through 63 and (name N or name CA o \ r name C or name O or name CB )) or resid 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 76 or (resid 7 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 78 through 9 \ 8 or (resid 99 through 100 and (name N or name CA or name C or name O or name CB \ )) or resid 101 through 103 or (resid 104 and (name N or name CA or name C or n \ ame O or name CB )) or resid 105 through 122 or (resid 123 and (name N or name C \ A or name C or name O or name CB )) or resid 124)) selection = (chain 'C' 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 25 or (resid 26 through 27 and (na \ me N or name CA or name C or name O or name CB )) or resid 28 through 37 or (res \ id 38 through 40 and (name N or name CA or name C or name O or name CB )) or res \ id 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or r \ esid 43 through 58 or (resid 59 through 63 and (name N or name CA or name C or n \ ame O or name CB )) or resid 64 through 91 or (resid 92 and (name N or name CA o \ r name C or name O or name CB )) or resid 93 through 95 or (resid 96 through 97 \ and (name N or name CA or name C or name O or name CB )) or resid 98 or (resid 9 \ 9 through 100 and (name N or name CA or name C or name O or name CB )) or resid \ 101 through 103 or (resid 104 and (name N or name CA or name C or name O or name \ CB )) or resid 105 through 122 or (resid 123 and (name N or name CA or name C o \ r name O or name CB )) or resid 124)) 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 25 or (resid 26 through 27 and (na \ me N or name CA or name C or name O or name CB )) or resid 28 through 37 or (res \ id 38 through 40 and (name N or name CA or name C or name O or name CB )) or res \ id 41 or (resid 42 and (name N or name CA or name C or name O or name CB )) or r \ esid 43 through 45 or (resid 46 and (name N or name CA or name C or name O or na \ me CB )) or resid 47 through 50 or (resid 51 and (name N or name CA or name C or \ name O or name CB )) or resid 52 through 58 or (resid 59 through 63 and (name N \ or name CA or name C or name O or name CB )) or resid 64 through 65 or (resid 6 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 67 through 7 \ 6 or (resid 77 and (name N or name CA or name C or name O or name CB )) or resid \ 78 through 95 or (resid 96 through 97 and (name N or name CA or name C or name \ O or name CB )) or resid 98 or (resid 99 through 100 and (name N or name CA or n \ ame C or name O or name CB )) or resid 101 through 124)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.120 Find NCS groups from input model: 0.230 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 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 : 0.006 0.109 3624 Z= 0.396 Angle : 0.621 10.259 4957 Z= 0.318 Chirality : 0.045 0.130 565 Planarity : 0.004 0.040 627 Dihedral : 13.407 82.301 1219 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 0.57 % Allowed : 0.00 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.38), residues: 458 helix: 0.66 (0.86), residues: 34 sheet: 2.28 (0.33), residues: 240 loop : -0.36 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 79 HIS 0.002 0.000 HIS D 90 PHE 0.009 0.001 PHE A 64 TYR 0.017 0.001 TYR B 78 ARG 0.004 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.415 Fit side-chains REVERT: C 44 PHE cc_start: 0.8001 (t80) cc_final: 0.7721 (t80) outliers start: 2 outliers final: 0 residues processed: 94 average time/residue: 0.1767 time to fit residues: 19.8851 Evaluate side-chains 77 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3624 Z= 0.243 Angle : 0.536 4.835 4957 Z= 0.280 Chirality : 0.048 0.138 565 Planarity : 0.004 0.039 627 Dihedral : 6.192 69.292 503 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.71 % Allowed : 10.26 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.38), residues: 458 helix: 1.39 (0.92), residues: 36 sheet: 2.35 (0.33), residues: 235 loop : -0.79 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 79 HIS 0.003 0.001 HIS A 88 PHE 0.010 0.002 PHE B 33 TYR 0.011 0.002 TYR B 116 ARG 0.003 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.364 Fit side-chains REVERT: C 44 PHE cc_start: 0.7949 (t80) cc_final: 0.7678 (t80) outliers start: 6 outliers final: 6 residues processed: 87 average time/residue: 0.1942 time to fit residues: 19.9135 Evaluate side-chains 83 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 40 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.7709 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3624 Z= 0.169 Angle : 0.471 3.861 4957 Z= 0.245 Chirality : 0.046 0.142 565 Planarity : 0.004 0.052 627 Dihedral : 5.558 65.843 503 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.42 % Allowed : 15.67 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.39), residues: 458 helix: 1.66 (0.94), residues: 36 sheet: 2.35 (0.33), residues: 235 loop : -0.91 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 79 HIS 0.003 0.001 HIS C 56 PHE 0.007 0.001 PHE A 64 TYR 0.009 0.001 TYR D 116 ARG 0.002 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.391 Fit side-chains REVERT: C 44 PHE cc_start: 0.7960 (t80) cc_final: 0.7686 (t80) outliers start: 5 outliers final: 3 residues processed: 85 average time/residue: 0.2009 time to fit residues: 20.0435 Evaluate side-chains 78 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain D residue 20 VAL 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: 0.7980 chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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: 0.7814 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3624 Z= 0.367 Angle : 0.586 5.559 4957 Z= 0.304 Chirality : 0.050 0.149 565 Planarity : 0.005 0.067 627 Dihedral : 6.014 66.073 503 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.85 % Allowed : 17.66 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.38), residues: 458 helix: 1.46 (0.93), residues: 36 sheet: 2.00 (0.34), residues: 219 loop : -0.97 (0.39), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 79 HIS 0.004 0.001 HIS B 31 PHE 0.012 0.002 PHE B 33 TYR 0.010 0.002 TYR B 116 ARG 0.002 0.000 ARG C 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.397 Fit side-chains REVERT: B 17 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7931 (mt) REVERT: C 44 PHE cc_start: 0.8006 (t80) cc_final: 0.7670 (t80) REVERT: D 84 ILE cc_start: 0.8080 (mt) cc_final: 0.7856 (mt) outliers start: 10 outliers final: 7 residues processed: 85 average time/residue: 0.1824 time to fit residues: 18.4013 Evaluate side-chains 81 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- 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: 0.7788 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3624 Z= 0.257 Angle : 0.517 4.673 4957 Z= 0.269 Chirality : 0.048 0.143 565 Planarity : 0.005 0.064 627 Dihedral : 5.665 59.490 503 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.56 % Allowed : 19.94 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.39), residues: 458 helix: 1.44 (0.92), residues: 36 sheet: 1.95 (0.34), residues: 219 loop : -1.01 (0.39), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 79 HIS 0.002 0.001 HIS B 31 PHE 0.009 0.002 PHE A 64 TYR 0.010 0.001 TYR D 116 ARG 0.004 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.426 Fit side-chains REVERT: C 44 PHE cc_start: 0.8010 (t80) cc_final: 0.7695 (t80) REVERT: D 84 ILE cc_start: 0.8076 (mt) cc_final: 0.7852 (mt) outliers start: 9 outliers final: 7 residues processed: 87 average time/residue: 0.1970 time to fit residues: 20.2395 Evaluate side-chains 84 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 106 THR 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: 6.9990 chunk 42 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.7867 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 3624 Z= 0.513 Angle : 0.676 7.587 4957 Z= 0.350 Chirality : 0.053 0.153 565 Planarity : 0.006 0.071 627 Dihedral : 6.422 69.682 503 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.27 % Allowed : 19.37 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.39), residues: 458 helix: 1.07 (0.88), residues: 36 sheet: 1.49 (0.35), residues: 217 loop : -1.22 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 79 HIS 0.006 0.002 HIS B 31 PHE 0.016 0.003 PHE B 33 TYR 0.012 0.002 TYR B 116 ARG 0.004 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.325 Fit side-chains REVERT: A 34 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7059 (ttt-90) REVERT: B 17 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7998 (mt) REVERT: C 42 GLU cc_start: 0.8022 (pt0) cc_final: 0.7715 (pt0) REVERT: C 44 PHE cc_start: 0.8073 (t80) cc_final: 0.7714 (t80) REVERT: D 84 ILE cc_start: 0.8171 (mt) cc_final: 0.7938 (mt) outliers start: 15 outliers final: 10 residues processed: 88 average time/residue: 0.1799 time to fit residues: 18.9738 Evaluate side-chains 90 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.7796 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3624 Z= 0.233 Angle : 0.518 5.573 4957 Z= 0.269 Chirality : 0.048 0.145 565 Planarity : 0.005 0.062 627 Dihedral : 5.684 58.761 503 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.27 % Allowed : 20.23 % Favored : 75.50 % 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: 0.71 (0.39), residues: 458 helix: 1.30 (0.90), residues: 36 sheet: 1.65 (0.35), residues: 222 loop : -1.15 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 79 HIS 0.002 0.001 HIS B 31 PHE 0.009 0.001 PHE A 64 TYR 0.009 0.001 TYR D 116 ARG 0.005 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.402 Fit side-chains REVERT: A 34 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7003 (ttt-90) REVERT: B 17 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7943 (mt) REVERT: C 42 GLU cc_start: 0.7925 (pt0) cc_final: 0.7489 (pt0) REVERT: C 44 PHE cc_start: 0.8029 (t80) cc_final: 0.7654 (t80) REVERT: D 84 ILE cc_start: 0.8134 (mt) cc_final: 0.7896 (mt) outliers start: 15 outliers final: 8 residues processed: 89 average time/residue: 0.1857 time to fit residues: 19.6685 Evaluate side-chains 88 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 20 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7764 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3624 Z= 0.188 Angle : 0.505 6.351 4957 Z= 0.260 Chirality : 0.047 0.143 565 Planarity : 0.005 0.061 627 Dihedral : 5.327 51.580 503 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.99 % Allowed : 20.23 % Favored : 75.78 % 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: 0.93 (0.39), residues: 458 helix: 1.48 (0.96), residues: 36 sheet: 1.76 (0.34), residues: 227 loop : -1.05 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 79 HIS 0.002 0.001 HIS D 90 PHE 0.007 0.001 PHE A 64 TYR 0.010 0.001 TYR D 116 ARG 0.003 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.634 Fit side-chains REVERT: A 34 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7005 (ttt-90) REVERT: B 17 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7924 (mt) REVERT: C 44 PHE cc_start: 0.8022 (t80) cc_final: 0.7695 (t80) REVERT: D 84 ILE cc_start: 0.8100 (mt) cc_final: 0.7868 (mt) REVERT: D 89 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6703 (mt-10) outliers start: 14 outliers final: 10 residues processed: 91 average time/residue: 0.1996 time to fit residues: 21.7737 Evaluate side-chains 92 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 106 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7699 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3624 Z= 0.141 Angle : 0.477 6.788 4957 Z= 0.246 Chirality : 0.046 0.140 565 Planarity : 0.005 0.057 627 Dihedral : 4.910 53.511 503 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.28 % Allowed : 21.65 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.39), residues: 458 helix: 1.52 (0.96), residues: 36 sheet: 2.01 (0.34), residues: 227 loop : -0.82 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 79 HIS 0.001 0.000 HIS D 90 PHE 0.005 0.001 PHE C 87 TYR 0.010 0.001 TYR D 116 ARG 0.003 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.404 Fit side-chains REVERT: A 34 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6997 (ttt-90) REVERT: C 44 PHE cc_start: 0.8023 (t80) cc_final: 0.7714 (t80) REVERT: D 89 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6515 (mt-10) outliers start: 8 outliers final: 7 residues processed: 82 average time/residue: 0.1918 time to fit residues: 18.5993 Evaluate side-chains 81 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 74 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.7799 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3624 Z= 0.296 Angle : 0.576 7.089 4957 Z= 0.294 Chirality : 0.048 0.142 565 Planarity : 0.005 0.066 627 Dihedral : 5.557 58.366 503 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.28 % Allowed : 22.22 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.40), residues: 458 helix: 1.66 (1.00), residues: 36 sheet: 1.87 (0.34), residues: 222 loop : -0.91 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 79 HIS 0.003 0.001 HIS B 31 PHE 0.011 0.002 PHE B 33 TYR 0.010 0.002 TYR D 116 ARG 0.006 0.001 ARG A 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 916 Ramachandran restraints generated. 458 Oldfield, 0 Emsley, 458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.365 Fit side-chains REVERT: A 34 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7076 (ttt-90) REVERT: C 44 PHE cc_start: 0.8043 (t80) cc_final: 0.7714 (t80) REVERT: D 76 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7981 (mttp) REVERT: D 84 ILE cc_start: 0.8157 (mt) cc_final: 0.7923 (mt) REVERT: D 89 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6664 (mt-10) outliers start: 8 outliers final: 7 residues processed: 80 average time/residue: 0.2047 time to fit residues: 19.2761 Evaluate side-chains 83 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 74 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.154204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.131748 restraints weight = 4910.076| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.51 r_work: 0.3586 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3624 Z= 0.178 Angle : 0.509 7.042 4957 Z= 0.261 Chirality : 0.047 0.139 565 Planarity : 0.005 0.059 627 Dihedral : 5.116 51.596 503 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.28 % Allowed : 22.79 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.40), residues: 458 helix: 1.66 (0.99), residues: 36 sheet: 1.93 (0.34), residues: 227 loop : -0.84 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 79 HIS 0.001 0.001 HIS A 88 PHE 0.006 0.001 PHE A 64 TYR 0.011 0.001 TYR D 116 ARG 0.004 0.000 ARG B 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1201.40 seconds wall clock time: 21 minutes 53.10 seconds (1313.10 seconds total)