Starting phenix.real_space_refine on Sun Mar 10 22:59:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8equ_28546/03_2024/8equ_28546_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8equ_28546/03_2024/8equ_28546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8equ_28546/03_2024/8equ_28546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8equ_28546/03_2024/8equ_28546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8equ_28546/03_2024/8equ_28546_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8equ_28546/03_2024/8equ_28546_neut_updated.pdb" } resolution = 2.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 32 5.16 5 C 3680 2.51 5 N 976 2.21 5 O 1074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 173": "OD1" <-> "OD2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "F GLU 80": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5764 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1563 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1563 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "C" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 506 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 74} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 395 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'TRANS': 78} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'UNK:plan-1': 79} Unresolved non-hydrogen planarities: 79 Chain: "E" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 395 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'TRANS': 78} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'UNK:plan-1': 79} Unresolved non-hydrogen planarities: 79 Chain: "F" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 506 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 74} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "G" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 395 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'TRANS': 78} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'UNK:plan-1': 79} Unresolved non-hydrogen planarities: 79 Chain: "H" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 395 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'TRANS': 78} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'UNK:plan-1': 79} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Time building chain proxies: 3.81, per 1000 atoms: 0.66 Number of scatterers: 5764 At special positions: 0 Unit cell: (90.308, 93.684, 89.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 2 15.00 O 1074 8.00 N 976 7.00 C 3680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 79 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 47 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 79 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 73 " distance=2.03 Simple disulfide: pdb=" SG CYS F 35 " - pdb=" SG CYS F 47 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 936.5 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1668 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 2 sheets defined 105.9% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 43 through 62 removed outlier: 3.754A pdb=" N LYS A 61 " --> pdb=" O SER A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 98 Processing helix chain 'A' and resid 106 through 133 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'B' and resid 43 through 62 removed outlier: 3.755A pdb=" N LYS B 61 " --> pdb=" O SER B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 98 Processing helix chain 'B' and resid 106 through 133 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'C' and resid 2 through 18 removed outlier: 3.502A pdb=" N ILE C 6 " --> pdb=" O LEU C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 36 removed outlier: 3.528A pdb=" N CYS C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 66 removed outlier: 4.298A pdb=" N ASP C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Proline residue: C 56 - end of helix Processing helix chain 'C' and resid 69 through 76 removed outlier: 3.561A pdb=" N LEU C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 18 Processing helix chain 'D' and resid 21 through 37 removed outlier: 3.731A pdb=" N UNK D 37 " --> pdb=" O UNK D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 75 removed outlier: 4.055A pdb=" N UNK D 46 " --> pdb=" O UNK D 42 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N UNK D 56 " --> pdb=" O UNK D 52 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N UNK D 57 " --> pdb=" O UNK D 53 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N UNK D 68 " --> pdb=" O UNK D 64 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N UNK D 69 " --> pdb=" O UNK D 65 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N UNK D 70 " --> pdb=" O UNK D 66 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N UNK D 71 " --> pdb=" O UNK D 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 18 Processing helix chain 'E' and resid 21 through 37 removed outlier: 3.732A pdb=" N UNK E 37 " --> pdb=" O UNK E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 75 removed outlier: 4.055A pdb=" N UNK E 46 " --> pdb=" O UNK E 42 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N UNK E 56 " --> pdb=" O UNK E 52 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N UNK E 57 " --> pdb=" O UNK E 53 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N UNK E 68 " --> pdb=" O UNK E 64 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N UNK E 69 " --> pdb=" O UNK E 65 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N UNK E 70 " --> pdb=" O UNK E 66 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N UNK E 71 " --> pdb=" O UNK E 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 18 removed outlier: 3.501A pdb=" N ILE F 6 " --> pdb=" O LEU F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 36 removed outlier: 3.529A pdb=" N CYS F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 66 removed outlier: 4.298A pdb=" N ASP F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) Proline residue: F 56 - end of helix Processing helix chain 'F' and resid 69 through 76 removed outlier: 3.560A pdb=" N LEU F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 18 Processing helix chain 'G' and resid 21 through 37 removed outlier: 3.732A pdb=" N UNK G 37 " --> pdb=" O UNK G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 75 removed outlier: 4.055A pdb=" N UNK G 46 " --> pdb=" O UNK G 42 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N UNK G 56 " --> pdb=" O UNK G 52 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N UNK G 57 " --> pdb=" O UNK G 53 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N UNK G 68 " --> pdb=" O UNK G 64 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N UNK G 69 " --> pdb=" O UNK G 65 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N UNK G 70 " --> pdb=" O UNK G 66 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N UNK G 71 " --> pdb=" O UNK G 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 18 Processing helix chain 'H' and resid 21 through 37 removed outlier: 3.732A pdb=" N UNK H 37 " --> pdb=" O UNK H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 75 removed outlier: 4.055A pdb=" N UNK H 46 " --> pdb=" O UNK H 42 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N UNK H 56 " --> pdb=" O UNK H 52 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N UNK H 57 " --> pdb=" O UNK H 53 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N UNK H 68 " --> pdb=" O UNK H 64 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N UNK H 69 " --> pdb=" O UNK H 65 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N UNK H 70 " --> pdb=" O UNK H 66 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N UNK H 71 " --> pdb=" O UNK H 67 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 155 through 160 removed outlier: 6.193A pdb=" N HIS A 150 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N CYS A 200 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 232 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR A 217 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE A 230 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 155 through 160 removed outlier: 6.194A pdb=" N HIS B 150 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N CYS B 200 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE B 232 " --> pdb=" O TYR B 215 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR B 217 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE B 230 " --> pdb=" O THR B 217 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1314 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: 1.64 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 966 1.32 - 1.44: 1530 1.44 - 1.57: 3320 1.57 - 1.70: 4 1.70 - 1.82: 38 Bond restraints: 5858 Sorted by residual: bond pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 1.332 1.429 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C30 PEE A 401 " pdb=" O3 PEE A 401 " ideal model delta sigma weight residual 1.327 1.411 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C30 PEE B 401 " pdb=" O3 PEE B 401 " ideal model delta sigma weight residual 1.327 1.411 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C LEU A 41 " pdb=" N PRO A 42 " ideal model delta sigma weight residual 1.333 1.358 -0.025 1.01e-02 9.80e+03 5.99e+00 ... (remaining 5853 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.94: 66 105.94 - 112.95: 3274 112.95 - 119.97: 1870 119.97 - 126.99: 2773 126.99 - 134.00: 57 Bond angle restraints: 8040 Sorted by residual: angle pdb=" O3P PEE B 401 " pdb=" P PEE B 401 " pdb=" O4P PEE B 401 " ideal model delta sigma weight residual 92.91 109.35 -16.44 3.00e+00 1.11e-01 3.00e+01 angle pdb=" O3P PEE A 401 " pdb=" P PEE A 401 " pdb=" O4P PEE A 401 " ideal model delta sigma weight residual 92.91 109.31 -16.40 3.00e+00 1.11e-01 2.99e+01 angle pdb=" CB MET A 125 " pdb=" CG MET A 125 " pdb=" SD MET A 125 " ideal model delta sigma weight residual 112.70 122.43 -9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" CB MET B 125 " pdb=" CG MET B 125 " pdb=" SD MET B 125 " ideal model delta sigma weight residual 112.70 122.40 -9.70 3.00e+00 1.11e-01 1.05e+01 angle pdb=" O1P PEE A 401 " pdb=" P PEE A 401 " pdb=" O2P PEE A 401 " ideal model delta sigma weight residual 119.43 109.80 9.63 3.00e+00 1.11e-01 1.03e+01 ... (remaining 8035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.18: 3365 28.18 - 56.37: 61 56.37 - 84.55: 18 84.55 - 112.73: 2 112.73 - 140.91: 4 Dihedral angle restraints: 3450 sinusoidal: 900 harmonic: 2550 Sorted by residual: dihedral pdb=" CB CYS F 4 " pdb=" SG CYS F 4 " pdb=" SG CYS F 79 " pdb=" CB CYS F 79 " ideal model delta sinusoidal sigma weight residual -86.00 -171.16 85.16 1 1.00e+01 1.00e-02 8.79e+01 dihedral pdb=" CB CYS C 4 " pdb=" SG CYS C 4 " pdb=" SG CYS C 79 " pdb=" CB CYS C 79 " ideal model delta sinusoidal sigma weight residual -86.00 -171.14 85.14 1 1.00e+01 1.00e-02 8.79e+01 dihedral pdb=" CB CYS C 35 " pdb=" SG CYS C 35 " pdb=" SG CYS C 47 " pdb=" CB CYS C 47 " ideal model delta sinusoidal sigma weight residual -86.00 -145.66 59.66 1 1.00e+01 1.00e-02 4.75e+01 ... (remaining 3447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 821 0.048 - 0.096: 159 0.096 - 0.144: 20 0.144 - 0.193: 0 0.193 - 0.241: 2 Chirality restraints: 1002 Sorted by residual: chirality pdb=" C2 PEE A 401 " pdb=" C1 PEE A 401 " pdb=" C3 PEE A 401 " pdb=" O2 PEE A 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.57 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C2 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C3 PEE B 401 " pdb=" O2 PEE B 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.57 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE A 169 " pdb=" N ILE A 169 " pdb=" C ILE A 169 " pdb=" CB ILE A 169 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 999 not shown) Planarity restraints: 1022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 41 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" C LEU B 41 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU B 41 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO B 42 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 41 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C LEU A 41 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU A 41 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO A 42 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 206 " 0.011 2.00e-02 2.50e+03 1.13e-02 2.55e+00 pdb=" CG TYR B 206 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 206 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 206 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 206 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 206 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 206 " -0.001 2.00e-02 2.50e+03 ... (remaining 1019 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1960 2.83 - 3.35: 5929 3.35 - 3.87: 9621 3.87 - 4.38: 9986 4.38 - 4.90: 17462 Nonbonded interactions: 44958 Sorted by model distance: nonbonded pdb=" O LYS A 198 " pdb=" OH TYR A 233 " model vdw 2.317 2.440 nonbonded pdb=" O LYS B 198 " pdb=" OH TYR B 233 " model vdw 2.317 2.440 nonbonded pdb=" OH TYR B 154 " pdb=" OE2 GLU B 191 " model vdw 2.344 2.440 nonbonded pdb=" OH TYR A 154 " pdb=" OE2 GLU A 191 " model vdw 2.344 2.440 nonbonded pdb=" OG1 THR A 164 " pdb=" O SER A 166 " model vdw 2.344 2.440 ... (remaining 44953 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.690 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.150 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 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 0.097 5858 Z= 0.261 Angle : 0.790 16.435 8040 Z= 0.382 Chirality : 0.040 0.241 1002 Planarity : 0.004 0.032 1022 Dihedral : 14.512 140.915 1764 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.36), residues: 530 helix: 0.76 (0.30), residues: 308 sheet: -0.26 (0.51), residues: 92 loop : -1.82 (0.49), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 193 HIS 0.004 0.001 HIS A 204 PHE 0.010 0.001 PHE B 56 TYR 0.028 0.002 TYR B 206 ARG 0.003 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7786 (mpp80) cc_final: 0.7553 (mpp80) REVERT: A 198 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7624 (mmmm) REVERT: A 210 ASP cc_start: 0.8189 (m-30) cc_final: 0.7947 (m-30) REVERT: A 213 GLN cc_start: 0.7923 (tt0) cc_final: 0.7377 (tp40) REVERT: B 198 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7628 (mmmm) REVERT: B 210 ASP cc_start: 0.8185 (m-30) cc_final: 0.7924 (m-30) REVERT: B 211 TYR cc_start: 0.8528 (m-80) cc_final: 0.8273 (m-80) REVERT: B 213 GLN cc_start: 0.7932 (tt0) cc_final: 0.7353 (tp40) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.8513 time to fit residues: 89.4110 Evaluate side-chains 75 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 93 HIS B 82 ASN B 93 HIS F 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 5858 Z= 0.432 Angle : 0.591 7.633 8040 Z= 0.302 Chirality : 0.039 0.136 1002 Planarity : 0.005 0.035 1022 Dihedral : 9.907 103.159 928 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.87 % Allowed : 11.21 % Favored : 86.92 % 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: 0.37 (0.36), residues: 530 helix: 1.29 (0.29), residues: 310 sheet: -0.66 (0.51), residues: 94 loop : -1.54 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 45 HIS 0.003 0.001 HIS A 182 PHE 0.025 0.003 PHE A 43 TYR 0.024 0.002 TYR A 215 ARG 0.003 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 45 TRP cc_start: 0.7122 (m100) cc_final: 0.6534 (m-10) REVERT: A 61 LYS cc_start: 0.8865 (mttm) cc_final: 0.8322 (mtmt) REVERT: A 128 TRP cc_start: 0.8022 (t60) cc_final: 0.7774 (t60) REVERT: A 198 LYS cc_start: 0.8365 (mtpt) cc_final: 0.8043 (mmmm) REVERT: A 213 GLN cc_start: 0.7971 (tt0) cc_final: 0.7675 (tt0) REVERT: B 45 TRP cc_start: 0.7201 (m100) cc_final: 0.6596 (m-10) REVERT: B 61 LYS cc_start: 0.8833 (mttm) cc_final: 0.8338 (mtmm) REVERT: B 128 TRP cc_start: 0.8049 (t60) cc_final: 0.7774 (t60) REVERT: B 198 LYS cc_start: 0.8330 (mtpt) cc_final: 0.7993 (mmmm) REVERT: B 213 GLN cc_start: 0.7985 (tt0) cc_final: 0.7685 (tt0) REVERT: C 9 ASP cc_start: 0.8575 (m-30) cc_final: 0.8320 (m-30) outliers start: 8 outliers final: 3 residues processed: 82 average time/residue: 1.0084 time to fit residues: 87.1264 Evaluate side-chains 73 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 222 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 20.0000 chunk 23 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 30.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 5858 Z= 0.404 Angle : 0.563 7.486 8040 Z= 0.287 Chirality : 0.038 0.142 1002 Planarity : 0.004 0.036 1022 Dihedral : 8.945 95.717 928 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.93 % Allowed : 15.42 % Favored : 83.64 % 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 (0.36), residues: 530 helix: 1.28 (0.29), residues: 308 sheet: -0.67 (0.51), residues: 94 loop : -1.48 (0.49), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 149 HIS 0.003 0.001 HIS B 93 PHE 0.014 0.003 PHE B 56 TYR 0.015 0.002 TYR B 215 ARG 0.004 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.559 Fit side-chains REVERT: A 61 LYS cc_start: 0.8902 (mttm) cc_final: 0.8385 (mtmt) REVERT: A 128 TRP cc_start: 0.8105 (t60) cc_final: 0.7767 (t60) REVERT: A 213 GLN cc_start: 0.7945 (tt0) cc_final: 0.7656 (tt0) REVERT: B 61 LYS cc_start: 0.8878 (mttm) cc_final: 0.8360 (mtmt) REVERT: B 128 TRP cc_start: 0.8100 (t60) cc_final: 0.7754 (t60) REVERT: B 213 GLN cc_start: 0.7949 (tt0) cc_final: 0.7661 (tt0) outliers start: 4 outliers final: 3 residues processed: 80 average time/residue: 0.9393 time to fit residues: 79.5422 Evaluate side-chains 72 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 222 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN B 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5858 Z= 0.290 Angle : 0.527 7.535 8040 Z= 0.264 Chirality : 0.035 0.149 1002 Planarity : 0.004 0.035 1022 Dihedral : 8.344 88.298 928 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.40 % Allowed : 17.29 % Favored : 81.31 % 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: 0.37 (0.36), residues: 530 helix: 1.38 (0.29), residues: 310 sheet: -0.80 (0.51), residues: 94 loop : -1.69 (0.48), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 149 HIS 0.002 0.001 HIS B 93 PHE 0.014 0.002 PHE A 56 TYR 0.009 0.001 TYR A 154 ARG 0.004 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.534 Fit side-chains REVERT: A 61 LYS cc_start: 0.8893 (mttm) cc_final: 0.8373 (mtmt) REVERT: A 128 TRP cc_start: 0.8086 (t60) cc_final: 0.7766 (t60) REVERT: A 213 GLN cc_start: 0.7902 (tt0) cc_final: 0.7601 (tt0) REVERT: B 61 LYS cc_start: 0.8885 (mttm) cc_final: 0.8353 (mtmt) REVERT: B 128 TRP cc_start: 0.8076 (t60) cc_final: 0.7712 (t60) REVERT: B 213 GLN cc_start: 0.7907 (tt0) cc_final: 0.7609 (tt0) outliers start: 6 outliers final: 3 residues processed: 75 average time/residue: 0.8314 time to fit residues: 66.4604 Evaluate side-chains 70 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 HIS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 222 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 59 optimal weight: 30.0000 chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.7425 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5858 Z= 0.338 Angle : 0.555 8.590 8040 Z= 0.277 Chirality : 0.036 0.162 1002 Planarity : 0.004 0.034 1022 Dihedral : 7.802 80.360 928 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.70 % Allowed : 19.63 % Favored : 79.67 % 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: 0.55 (0.36), residues: 530 helix: 1.49 (0.30), residues: 306 sheet: -0.87 (0.53), residues: 90 loop : -1.27 (0.49), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 131 HIS 0.003 0.001 HIS B 78 PHE 0.014 0.002 PHE B 56 TYR 0.011 0.001 TYR B 206 ARG 0.003 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.511 Fit side-chains REVERT: A 61 LYS cc_start: 0.8904 (mttm) cc_final: 0.8368 (mtmt) REVERT: A 128 TRP cc_start: 0.8123 (t60) cc_final: 0.7731 (t60) REVERT: A 213 GLN cc_start: 0.7938 (tt0) cc_final: 0.7657 (tt0) REVERT: B 61 LYS cc_start: 0.8901 (mttm) cc_final: 0.8369 (mtmt) REVERT: B 128 TRP cc_start: 0.8116 (t60) cc_final: 0.7771 (t60) REVERT: B 213 GLN cc_start: 0.7942 (tt0) cc_final: 0.7626 (tt0) outliers start: 3 outliers final: 2 residues processed: 70 average time/residue: 0.9054 time to fit residues: 67.4822 Evaluate side-chains 68 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 222 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 30.0000 chunk 19 optimal weight: 0.1980 chunk 79 optimal weight: 30.0000 chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 41 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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: 0.7421 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5858 Z= 0.299 Angle : 0.539 8.153 8040 Z= 0.269 Chirality : 0.035 0.167 1002 Planarity : 0.004 0.033 1022 Dihedral : 7.331 71.211 928 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.87 % Allowed : 20.09 % Favored : 78.04 % 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: 0.61 (0.37), residues: 530 helix: 1.59 (0.30), residues: 306 sheet: -0.91 (0.52), residues: 94 loop : -1.35 (0.49), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 131 HIS 0.002 0.001 HIS B 93 PHE 0.014 0.002 PHE A 56 TYR 0.014 0.001 TYR A 154 ARG 0.003 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.563 Fit side-chains REVERT: A 61 LYS cc_start: 0.8914 (mttm) cc_final: 0.8356 (mtmt) REVERT: A 128 TRP cc_start: 0.8101 (t60) cc_final: 0.7764 (t60) REVERT: A 213 GLN cc_start: 0.7944 (tt0) cc_final: 0.7596 (tt0) REVERT: B 61 LYS cc_start: 0.8909 (mttm) cc_final: 0.8358 (mtmt) REVERT: B 128 TRP cc_start: 0.8095 (t60) cc_final: 0.7754 (t60) REVERT: B 134 ARG cc_start: 0.7623 (mmm-85) cc_final: 0.7394 (mmm-85) REVERT: B 213 GLN cc_start: 0.7941 (tt0) cc_final: 0.7593 (tt0) outliers start: 8 outliers final: 4 residues processed: 76 average time/residue: 0.8365 time to fit residues: 67.9349 Evaluate side-chains 71 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 HIS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 74 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 57 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 79 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 20.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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: 0.7458 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 5858 Z= 0.557 Angle : 0.645 8.831 8040 Z= 0.323 Chirality : 0.040 0.176 1002 Planarity : 0.004 0.035 1022 Dihedral : 7.417 68.913 928 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.97 % Allowed : 18.46 % Favored : 77.57 % 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: 0.34 (0.36), residues: 530 helix: 1.26 (0.30), residues: 306 sheet: -0.81 (0.53), residues: 94 loop : -1.31 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 131 HIS 0.004 0.002 HIS A 78 PHE 0.015 0.003 PHE A 146 TYR 0.015 0.002 TYR A 109 ARG 0.003 0.001 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.551 Fit side-chains REVERT: A 61 LYS cc_start: 0.8879 (mttm) cc_final: 0.8338 (mtmt) REVERT: A 128 TRP cc_start: 0.8217 (t60) cc_final: 0.7887 (t60) REVERT: A 213 GLN cc_start: 0.7958 (tt0) cc_final: 0.7626 (tt0) REVERT: B 61 LYS cc_start: 0.8869 (mttm) cc_final: 0.8324 (mtmt) REVERT: B 128 TRP cc_start: 0.8216 (t60) cc_final: 0.7889 (t60) REVERT: B 134 ARG cc_start: 0.7646 (mmm-85) cc_final: 0.7436 (mmm-85) REVERT: B 182 HIS cc_start: 0.7327 (m-70) cc_final: 0.7116 (m-70) REVERT: B 194 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7845 (mm-30) REVERT: B 213 GLN cc_start: 0.7944 (tt0) cc_final: 0.7615 (tt0) REVERT: C 4 CYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7733 (t) REVERT: F 4 CYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7762 (t) outliers start: 17 outliers final: 8 residues processed: 82 average time/residue: 0.9036 time to fit residues: 78.4899 Evaluate side-chains 79 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 182 HIS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain F residue 4 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 5858 Z= 0.541 Angle : 0.643 9.681 8040 Z= 0.320 Chirality : 0.040 0.182 1002 Planarity : 0.004 0.040 1022 Dihedral : 7.067 63.321 928 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.74 % Allowed : 18.93 % Favored : 77.34 % 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: 0.33 (0.37), residues: 530 helix: 1.16 (0.29), residues: 306 sheet: -0.63 (0.54), residues: 102 loop : -1.22 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 131 HIS 0.003 0.001 HIS A 150 PHE 0.014 0.003 PHE B 56 TYR 0.011 0.002 TYR B 211 ARG 0.004 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.493 Fit side-chains REVERT: A 61 LYS cc_start: 0.8879 (mttm) cc_final: 0.8345 (mtmt) REVERT: A 128 TRP cc_start: 0.8180 (t60) cc_final: 0.7828 (t60) REVERT: A 213 GLN cc_start: 0.7944 (tt0) cc_final: 0.7606 (tt0) REVERT: B 61 LYS cc_start: 0.8872 (mttm) cc_final: 0.8338 (mtmt) REVERT: B 128 TRP cc_start: 0.8176 (t60) cc_final: 0.7820 (t60) REVERT: B 194 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7827 (mm-30) REVERT: B 213 GLN cc_start: 0.7948 (tt0) cc_final: 0.7612 (tt0) REVERT: C 4 CYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7720 (t) REVERT: F 4 CYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7750 (t) outliers start: 16 outliers final: 8 residues processed: 78 average time/residue: 1.0734 time to fit residues: 88.1080 Evaluate side-chains 76 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain F residue 4 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 30.0000 chunk 44 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 30.0000 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 0.0980 chunk 69 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 77 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 overall best weight: 6.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.140 5858 Z= 1.212 Angle : 0.953 11.226 8040 Z= 0.472 Chirality : 0.056 0.231 1002 Planarity : 0.006 0.040 1022 Dihedral : 7.399 62.494 928 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.80 % Allowed : 20.33 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.36), residues: 530 helix: 0.58 (0.29), residues: 304 sheet: -0.64 (0.54), residues: 102 loop : -1.04 (0.52), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 131 HIS 0.007 0.003 HIS A 78 PHE 0.019 0.004 PHE A 230 TYR 0.021 0.003 TYR B 109 ARG 0.010 0.002 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.605 Fit side-chains REVERT: A 61 LYS cc_start: 0.8912 (mttm) cc_final: 0.8315 (mtmt) REVERT: A 91 TYR cc_start: 0.7607 (t80) cc_final: 0.7357 (t80) REVERT: A 128 TRP cc_start: 0.8261 (t60) cc_final: 0.8017 (t60) REVERT: A 213 GLN cc_start: 0.8030 (tt0) cc_final: 0.7740 (tt0) REVERT: B 61 LYS cc_start: 0.8940 (mttm) cc_final: 0.8328 (mtmt) REVERT: B 91 TYR cc_start: 0.7641 (t80) cc_final: 0.7431 (t80) REVERT: B 128 TRP cc_start: 0.8260 (t60) cc_final: 0.8014 (t60) REVERT: B 182 HIS cc_start: 0.7528 (m-70) cc_final: 0.7212 (m90) REVERT: B 192 LYS cc_start: 0.8831 (tptm) cc_final: 0.8597 (tttp) REVERT: B 194 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7864 (mm-30) REVERT: B 213 GLN cc_start: 0.8031 (tt0) cc_final: 0.7747 (tt0) REVERT: C 4 CYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7856 (t) REVERT: F 4 CYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7887 (t) outliers start: 12 outliers final: 8 residues processed: 76 average time/residue: 1.0677 time to fit residues: 85.5142 Evaluate side-chains 77 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain F residue 4 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 chunk 39 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 19 optimal weight: 0.6980 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 5858 Z= 0.436 Angle : 0.647 9.994 8040 Z= 0.321 Chirality : 0.038 0.178 1002 Planarity : 0.004 0.038 1022 Dihedral : 6.903 58.915 928 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.57 % Allowed : 19.63 % Favored : 77.80 % 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 (0.36), residues: 530 helix: 0.86 (0.29), residues: 308 sheet: -0.91 (0.52), residues: 94 loop : -1.34 (0.49), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 149 HIS 0.003 0.001 HIS B 93 PHE 0.015 0.003 PHE B 56 TYR 0.016 0.002 TYR A 154 ARG 0.003 0.001 ARG A 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.569 Fit side-chains REVERT: A 61 LYS cc_start: 0.8875 (mttm) cc_final: 0.8308 (mtmt) REVERT: A 128 TRP cc_start: 0.8199 (t60) cc_final: 0.7852 (t60) REVERT: A 213 GLN cc_start: 0.7919 (tt0) cc_final: 0.7586 (tt0) REVERT: B 61 LYS cc_start: 0.8875 (mttm) cc_final: 0.8311 (mtmt) REVERT: B 128 TRP cc_start: 0.8175 (t60) cc_final: 0.7820 (t60) REVERT: B 194 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7816 (mm-30) REVERT: B 213 GLN cc_start: 0.7924 (tt0) cc_final: 0.7589 (tt0) REVERT: C 4 CYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7713 (t) REVERT: F 4 CYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7732 (t) outliers start: 11 outliers final: 7 residues processed: 72 average time/residue: 0.8985 time to fit residues: 68.8022 Evaluate side-chains 71 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain F residue 4 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 20.0000 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 57 optimal weight: 30.0000 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS B 78 HIS B 82 ASN B 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.188054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.111933 restraints weight = 7008.348| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.40 r_work: 0.3027 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5858 Z= 0.216 Angle : 0.586 9.921 8040 Z= 0.287 Chirality : 0.034 0.165 1002 Planarity : 0.004 0.037 1022 Dihedral : 6.390 53.443 928 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.10 % Allowed : 21.26 % Favored : 76.64 % 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 (0.36), residues: 530 helix: 1.21 (0.30), residues: 308 sheet: -0.86 (0.53), residues: 94 loop : -1.59 (0.48), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 149 HIS 0.003 0.001 HIS B 204 PHE 0.014 0.002 PHE B 56 TYR 0.015 0.001 TYR A 154 ARG 0.006 0.001 ARG A 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2055.87 seconds wall clock time: 37 minutes 23.23 seconds (2243.23 seconds total)