Starting phenix.real_space_refine on Wed Aug 7 19:30:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/08_2024/8ump_42381.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/08_2024/8ump_42381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/08_2024/8ump_42381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/08_2024/8ump_42381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/08_2024/8ump_42381.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/08_2024/8ump_42381.cif" } resolution = 2.92 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= 0.003 sd= 0.046 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 24 5.16 5 C 13764 2.51 5 N 3564 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 21432 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "B" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "E" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "F" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "G" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "I" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "J" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "K" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "N" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "O" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "P" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "Q" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "R" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "S" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "T" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "U" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "V" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "W" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "X" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Time building chain proxies: 12.49, per 1000 atoms: 0.58 Number of scatterers: 21432 At special positions: 0 Unit cell: (138.938, 131.625, 126.75, 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 24 16.00 O 4080 8.00 N 3564 7.00 C 13764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.72 Conformation dependent library (CDL) restraints added in 3.7 seconds 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5232 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 24 sheets defined 66.1% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 Processing helix chain 'A' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 52 Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'C' and resid 2 through 17 Processing helix chain 'C' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 71 through 85 Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 105 through 121 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'E' and resid 2 through 17 Processing helix chain 'E' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 52 Processing helix chain 'E' and resid 53 through 68 Processing helix chain 'E' and resid 71 through 85 Processing helix chain 'E' and resid 87 through 102 Processing helix chain 'E' and resid 105 through 121 Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 83 through 95 Processing helix chain 'F' and resid 112 through 121 Processing helix chain 'G' and resid 2 through 17 Processing helix chain 'G' and resid 19 through 34 removed outlier: 3.776A pdb=" N LYS G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 52 Processing helix chain 'G' and resid 53 through 68 Processing helix chain 'G' and resid 71 through 85 Processing helix chain 'G' and resid 87 through 102 Processing helix chain 'G' and resid 105 through 121 Processing helix chain 'H' and resid 32 through 46 Processing helix chain 'H' and resid 83 through 95 Processing helix chain 'H' and resid 112 through 121 Processing helix chain 'I' and resid 2 through 17 Processing helix chain 'I' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS I 33 " --> pdb=" O LEU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 52 Processing helix chain 'I' and resid 53 through 68 Processing helix chain 'I' and resid 71 through 85 Processing helix chain 'I' and resid 87 through 102 Processing helix chain 'I' and resid 105 through 121 Processing helix chain 'J' and resid 32 through 46 Processing helix chain 'J' and resid 83 through 95 Processing helix chain 'J' and resid 112 through 121 Processing helix chain 'K' and resid 2 through 17 Processing helix chain 'K' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 52 Processing helix chain 'K' and resid 53 through 68 Processing helix chain 'K' and resid 71 through 85 Processing helix chain 'K' and resid 87 through 102 Processing helix chain 'K' and resid 105 through 121 Processing helix chain 'L' and resid 32 through 46 Processing helix chain 'L' and resid 83 through 95 Processing helix chain 'L' and resid 112 through 121 Processing helix chain 'M' and resid 2 through 17 Processing helix chain 'M' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS M 33 " --> pdb=" O LEU M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 52 Processing helix chain 'M' and resid 53 through 68 Processing helix chain 'M' and resid 71 through 85 Processing helix chain 'M' and resid 87 through 102 Processing helix chain 'M' and resid 105 through 121 Processing helix chain 'N' and resid 32 through 46 Processing helix chain 'N' and resid 83 through 95 Processing helix chain 'N' and resid 112 through 121 Processing helix chain 'O' and resid 2 through 17 Processing helix chain 'O' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 52 Processing helix chain 'O' and resid 53 through 68 Processing helix chain 'O' and resid 71 through 85 Processing helix chain 'O' and resid 87 through 102 Processing helix chain 'O' and resid 105 through 121 Processing helix chain 'P' and resid 32 through 46 Processing helix chain 'P' and resid 83 through 95 Processing helix chain 'P' and resid 112 through 121 Processing helix chain 'Q' and resid 2 through 17 Processing helix chain 'Q' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS Q 33 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 52 Processing helix chain 'Q' and resid 53 through 68 Processing helix chain 'Q' and resid 71 through 85 Processing helix chain 'Q' and resid 87 through 102 Processing helix chain 'Q' and resid 105 through 121 Processing helix chain 'R' and resid 32 through 46 Processing helix chain 'R' and resid 83 through 95 Processing helix chain 'R' and resid 112 through 121 Processing helix chain 'S' and resid 2 through 17 Processing helix chain 'S' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS S 33 " --> pdb=" O LEU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 52 Processing helix chain 'S' and resid 53 through 68 Processing helix chain 'S' and resid 71 through 85 Processing helix chain 'S' and resid 87 through 102 Processing helix chain 'S' and resid 105 through 121 Processing helix chain 'T' and resid 32 through 46 Processing helix chain 'T' and resid 83 through 95 Processing helix chain 'T' and resid 112 through 121 Processing helix chain 'U' and resid 2 through 17 Processing helix chain 'U' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS U 33 " --> pdb=" O LEU U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 52 Processing helix chain 'U' and resid 53 through 68 Processing helix chain 'U' and resid 71 through 85 Processing helix chain 'U' and resid 87 through 102 Processing helix chain 'U' and resid 105 through 121 Processing helix chain 'V' and resid 32 through 46 Processing helix chain 'V' and resid 83 through 95 Processing helix chain 'V' and resid 112 through 121 Processing helix chain 'W' and resid 2 through 17 Processing helix chain 'W' and resid 19 through 34 removed outlier: 3.777A pdb=" N LYS W 33 " --> pdb=" O LEU W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 52 Processing helix chain 'W' and resid 53 through 68 Processing helix chain 'W' and resid 71 through 85 Processing helix chain 'W' and resid 87 through 102 Processing helix chain 'W' and resid 105 through 121 Processing helix chain 'X' and resid 32 through 46 Processing helix chain 'X' and resid 83 through 95 Processing helix chain 'X' and resid 112 through 121 Processing sheet with id=1, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=2, first strand: chain 'B' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU B 51 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'D' and resid 17 through 19 Processing sheet with id=4, first strand: chain 'D' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU D 51 " --> pdb=" O LYS D 78 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'F' and resid 17 through 19 Processing sheet with id=6, first strand: chain 'F' and resid 51 through 63 removed outlier: 3.796A pdb=" N GLU F 51 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=8, first strand: chain 'H' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU H 51 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=10, first strand: chain 'J' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU J 51 " --> pdb=" O LYS J 78 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'L' and resid 17 through 19 Processing sheet with id=12, first strand: chain 'L' and resid 51 through 63 removed outlier: 3.798A pdb=" N GLU L 51 " --> pdb=" O LYS L 78 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'N' and resid 17 through 19 Processing sheet with id=14, first strand: chain 'N' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU N 51 " --> pdb=" O LYS N 78 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'P' and resid 17 through 19 Processing sheet with id=16, first strand: chain 'P' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU P 51 " --> pdb=" O LYS P 78 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'R' and resid 17 through 19 Processing sheet with id=18, first strand: chain 'R' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU R 51 " --> pdb=" O LYS R 78 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'T' and resid 17 through 19 Processing sheet with id=20, first strand: chain 'T' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU T 51 " --> pdb=" O LYS T 78 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'V' and resid 17 through 19 Processing sheet with id=22, first strand: chain 'V' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU V 51 " --> pdb=" O LYS V 78 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'X' and resid 17 through 19 Processing sheet with id=24, first strand: chain 'X' and resid 51 through 63 removed outlier: 3.797A pdb=" N GLU X 51 " --> pdb=" O LYS X 78 " (cutoff:3.500A) 1632 hydrogen bonds defined for protein. 4824 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: 6.69 Time building geometry restraints manager: 8.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6996 1.34 - 1.46: 4834 1.46 - 1.58: 9926 1.58 - 1.70: 12 1.70 - 1.82: 36 Bond restraints: 21804 Sorted by residual: bond pdb=" CB PRO X 100 " pdb=" CG PRO X 100 " ideal model delta sigma weight residual 1.492 1.656 -0.164 5.00e-02 4.00e+02 1.07e+01 bond pdb=" CB PRO R 100 " pdb=" CG PRO R 100 " ideal model delta sigma weight residual 1.492 1.656 -0.164 5.00e-02 4.00e+02 1.07e+01 bond pdb=" CB PRO P 100 " pdb=" CG PRO P 100 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.07e+01 bond pdb=" CB PRO D 100 " pdb=" CG PRO D 100 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.07e+01 bond pdb=" CB PRO L 100 " pdb=" CG PRO L 100 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.07e+01 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 95.17 - 103.42: 214 103.42 - 111.66: 10649 111.66 - 119.91: 8689 119.91 - 128.15: 9968 128.15 - 136.39: 132 Bond angle restraints: 29652 Sorted by residual: angle pdb=" CA PRO L 100 " pdb=" N PRO L 100 " pdb=" CD PRO L 100 " ideal model delta sigma weight residual 112.00 96.97 15.03 1.40e+00 5.10e-01 1.15e+02 angle pdb=" CA PRO P 100 " pdb=" N PRO P 100 " pdb=" CD PRO P 100 " ideal model delta sigma weight residual 112.00 96.97 15.03 1.40e+00 5.10e-01 1.15e+02 angle pdb=" CA PRO X 100 " pdb=" N PRO X 100 " pdb=" CD PRO X 100 " ideal model delta sigma weight residual 112.00 96.97 15.03 1.40e+00 5.10e-01 1.15e+02 angle pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" CD PRO N 100 " ideal model delta sigma weight residual 112.00 96.97 15.03 1.40e+00 5.10e-01 1.15e+02 angle pdb=" CA PRO R 100 " pdb=" N PRO R 100 " pdb=" CD PRO R 100 " ideal model delta sigma weight residual 112.00 96.98 15.02 1.40e+00 5.10e-01 1.15e+02 ... (remaining 29647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 11030 17.47 - 34.93: 1570 34.93 - 52.40: 480 52.40 - 69.86: 132 69.86 - 87.33: 36 Dihedral angle restraints: 13248 sinusoidal: 5160 harmonic: 8088 Sorted by residual: dihedral pdb=" CA ASN W 37 " pdb=" CB ASN W 37 " pdb=" CG ASN W 37 " pdb=" OD1 ASN W 37 " ideal model delta sinusoidal sigma weight residual 120.00 -172.87 -67.13 2 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASN G 37 " pdb=" CB ASN G 37 " pdb=" CG ASN G 37 " pdb=" OD1 ASN G 37 " ideal model delta sinusoidal sigma weight residual 120.00 -172.88 -67.12 2 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASN M 37 " pdb=" CB ASN M 37 " pdb=" CG ASN M 37 " pdb=" OD1 ASN M 37 " ideal model delta sinusoidal sigma weight residual 120.00 -172.88 -67.12 2 2.00e+01 2.50e-03 1.02e+01 ... (remaining 13245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3059 0.055 - 0.109: 365 0.109 - 0.163: 32 0.163 - 0.218: 0 0.218 - 0.272: 12 Chirality restraints: 3468 Sorted by residual: chirality pdb=" CA PRO X 100 " pdb=" N PRO X 100 " pdb=" C PRO X 100 " pdb=" CB PRO X 100 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA PRO P 100 " pdb=" N PRO P 100 " pdb=" C PRO P 100 " pdb=" CB PRO P 100 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA PRO F 100 " pdb=" N PRO F 100 " pdb=" C PRO F 100 " pdb=" CB PRO F 100 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3465 not shown) Planarity restraints: 3756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 99 " 0.060 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO F 100 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO F 100 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 100 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU X 99 " -0.060 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO X 100 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO X 100 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO X 100 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 99 " -0.060 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO L 100 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO L 100 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 100 " -0.045 5.00e-02 4.00e+02 ... (remaining 3753 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3588 2.76 - 3.30: 19386 3.30 - 3.83: 35702 3.83 - 4.37: 44025 4.37 - 4.90: 78625 Nonbonded interactions: 181326 Sorted by model distance: nonbonded pdb=" OH TYR I 76 " pdb=" OE2 GLU J 45 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR U 76 " pdb=" OE2 GLU V 45 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR G 76 " pdb=" OE2 GLU H 45 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR S 76 " pdb=" OE2 GLU T 45 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR C 76 " pdb=" OE2 GLU D 45 " model vdw 2.227 3.040 ... (remaining 181321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } 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: 1.880 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: 0.960 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 56.120 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 : 0.007 0.164 21804 Z= 0.445 Angle : 0.736 15.033 29652 Z= 0.390 Chirality : 0.041 0.272 3468 Planarity : 0.006 0.081 3756 Dihedral : 19.060 87.331 8016 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 0.69 % Allowed : 32.88 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.15), residues: 2676 helix: 1.38 (0.11), residues: 1764 sheet: -0.63 (0.25), residues: 348 loop : 0.14 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 90 HIS 0.002 0.001 HIS F 95 PHE 0.008 0.001 PHE D 77 TYR 0.016 0.002 TYR X 73 ARG 0.011 0.001 ARG P 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 260 time to evaluate : 2.382 Fit side-chains REVERT: G 5 GLU cc_start: 0.7655 (mp0) cc_final: 0.7157 (mm-30) REVERT: K 5 GLU cc_start: 0.7585 (mp0) cc_final: 0.7253 (mm-30) REVERT: N 115 ARG cc_start: 0.7073 (ttt-90) cc_final: 0.6760 (ttt-90) REVERT: O 5 GLU cc_start: 0.7624 (mp0) cc_final: 0.7250 (mm-30) REVERT: P 81 ARG cc_start: 0.7986 (ptp90) cc_final: 0.7771 (ptt-90) REVERT: V 83 ARG cc_start: 0.8663 (mtp180) cc_final: 0.8373 (mmt180) outliers start: 15 outliers final: 2 residues processed: 261 average time/residue: 1.4158 time to fit residues: 416.4403 Evaluate side-chains 226 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain U residue 89 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 106 optimal weight: 0.2980 chunk 206 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 239 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN C 19 ASN C 37 ASN E 37 ASN G 37 ASN I 37 ASN K 37 ASN M 37 ASN O 37 ASN Q 37 ASN S 37 ASN U 37 ASN W 37 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21804 Z= 0.192 Angle : 0.472 5.212 29652 Z= 0.246 Chirality : 0.036 0.129 3468 Planarity : 0.003 0.040 3756 Dihedral : 3.735 24.358 2992 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 3.89 % Allowed : 23.86 % Favored : 72.25 % 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: 2.32 (0.16), residues: 2676 helix: 2.22 (0.11), residues: 1824 sheet: 0.14 (0.27), residues: 324 loop : 0.12 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 75 HIS 0.000 0.000 HIS J 95 PHE 0.012 0.002 PHE J 77 TYR 0.016 0.001 TYR O 76 ARG 0.006 0.001 ARG N 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 303 time to evaluate : 2.393 Fit side-chains REVERT: B 73 TYR cc_start: 0.8760 (m-80) cc_final: 0.8522 (m-80) REVERT: B 94 ARG cc_start: 0.8486 (mmm160) cc_final: 0.8212 (mmm-85) REVERT: B 100 PRO cc_start: 0.7939 (Cg_endo) cc_final: 0.7593 (Cg_exo) REVERT: D 94 ARG cc_start: 0.8507 (mmm160) cc_final: 0.8113 (mmm-85) REVERT: F 100 PRO cc_start: 0.7940 (Cg_endo) cc_final: 0.7572 (Cg_exo) REVERT: G 5 GLU cc_start: 0.7753 (mp0) cc_final: 0.7255 (mm-30) REVERT: H 100 PRO cc_start: 0.7808 (Cg_endo) cc_final: 0.7459 (Cg_exo) REVERT: J 74 ARG cc_start: 0.8346 (ttm170) cc_final: 0.8027 (ttm170) REVERT: J 94 ARG cc_start: 0.8555 (mmm160) cc_final: 0.8255 (mmm-85) REVERT: K 5 GLU cc_start: 0.7668 (mp0) cc_final: 0.7239 (mm-30) REVERT: N 94 ARG cc_start: 0.8456 (mmm160) cc_final: 0.8180 (mmm-85) REVERT: N 115 ARG cc_start: 0.6983 (ttt-90) cc_final: 0.6543 (ttt-90) REVERT: N 119 ARG cc_start: 0.6676 (mtm180) cc_final: 0.6462 (mtm110) REVERT: O 5 GLU cc_start: 0.7623 (mp0) cc_final: 0.7250 (mm-30) REVERT: P 83 ARG cc_start: 0.8258 (mmm160) cc_final: 0.8014 (mtp180) REVERT: P 94 ARG cc_start: 0.8558 (mmm160) cc_final: 0.8309 (mmm-85) REVERT: P 100 PRO cc_start: 0.7834 (Cg_endo) cc_final: 0.7502 (Cg_exo) REVERT: R 94 ARG cc_start: 0.8572 (mmm160) cc_final: 0.8335 (mmm-85) REVERT: S 5 GLU cc_start: 0.7641 (mp0) cc_final: 0.7175 (mm-30) REVERT: T 74 ARG cc_start: 0.8343 (ttm170) cc_final: 0.8139 (ttm170) REVERT: T 94 ARG cc_start: 0.8516 (mmm160) cc_final: 0.8227 (mmm-85) REVERT: V 92 GLN cc_start: 0.8030 (mt0) cc_final: 0.7813 (mm110) REVERT: W 5 GLU cc_start: 0.7696 (mp0) cc_final: 0.7214 (mm-30) REVERT: W 32 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7442 (mp) REVERT: X 100 PRO cc_start: 0.7838 (Cg_endo) cc_final: 0.7497 (Cg_exo) outliers start: 85 outliers final: 24 residues processed: 336 average time/residue: 2.1073 time to fit residues: 767.9551 Evaluate side-chains 242 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 217 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 45 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 199 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 240 optimal weight: 4.9990 chunk 259 optimal weight: 6.9990 chunk 213 optimal weight: 7.9990 chunk 238 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN D 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21804 Z= 0.173 Angle : 0.445 5.766 29652 Z= 0.230 Chirality : 0.035 0.133 3468 Planarity : 0.004 0.045 3756 Dihedral : 3.475 14.723 2988 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.89 % Allowed : 24.59 % Favored : 71.52 % 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: 2.79 (0.16), residues: 2676 helix: 2.62 (0.11), residues: 1824 sheet: 0.08 (0.29), residues: 348 loop : 0.28 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 117 HIS 0.001 0.001 HIS H 95 PHE 0.011 0.001 PHE P 77 TYR 0.014 0.001 TYR I 76 ARG 0.007 0.001 ARG R 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 286 time to evaluate : 2.515 Fit side-chains REVERT: A 106 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7993 (ptpp) REVERT: B 94 ARG cc_start: 0.8590 (mmm160) cc_final: 0.8302 (mmm-85) REVERT: B 100 PRO cc_start: 0.7902 (Cg_endo) cc_final: 0.7623 (Cg_exo) REVERT: E 5 GLU cc_start: 0.7749 (mp0) cc_final: 0.7311 (mm-30) REVERT: F 100 PRO cc_start: 0.7912 (Cg_endo) cc_final: 0.7630 (Cg_exo) REVERT: G 5 GLU cc_start: 0.7771 (mp0) cc_final: 0.7310 (mm-30) REVERT: H 100 PRO cc_start: 0.7686 (Cg_endo) cc_final: 0.7395 (Cg_exo) REVERT: I 5 GLU cc_start: 0.7701 (mp0) cc_final: 0.7468 (mp0) REVERT: J 100 PRO cc_start: 0.7924 (Cg_endo) cc_final: 0.7553 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7728 (mp0) cc_final: 0.7319 (mm-30) REVERT: M 33 LYS cc_start: 0.7393 (mptt) cc_final: 0.6758 (mmmm) REVERT: O 5 GLU cc_start: 0.7732 (mp0) cc_final: 0.7358 (mm-30) REVERT: P 74 ARG cc_start: 0.8375 (ttm170) cc_final: 0.8098 (ttm170) REVERT: P 94 ARG cc_start: 0.8620 (mmm160) cc_final: 0.8399 (mmm-85) REVERT: P 100 PRO cc_start: 0.7699 (Cg_endo) cc_final: 0.7452 (Cg_exo) REVERT: Q 5 GLU cc_start: 0.7822 (mp0) cc_final: 0.7371 (mm-30) REVERT: R 94 ARG cc_start: 0.8585 (mmm160) cc_final: 0.8360 (mmm-85) REVERT: S 5 GLU cc_start: 0.7740 (mp0) cc_final: 0.7294 (mm-30) REVERT: T 94 ARG cc_start: 0.8583 (mmm160) cc_final: 0.8282 (mmm-85) REVERT: V 45 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7836 (pt0) REVERT: V 92 GLN cc_start: 0.7978 (mt0) cc_final: 0.7690 (mm110) REVERT: W 5 GLU cc_start: 0.7730 (mp0) cc_final: 0.7272 (mm-30) REVERT: W 106 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.8057 (ptpp) REVERT: X 100 PRO cc_start: 0.7778 (Cg_endo) cc_final: 0.7523 (Cg_exo) outliers start: 85 outliers final: 27 residues processed: 329 average time/residue: 1.8606 time to fit residues: 670.1824 Evaluate side-chains 248 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 218 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 106 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 6.9990 chunk 180 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 241 optimal weight: 8.9990 chunk 255 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 228 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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: 0.8330 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21804 Z= 0.214 Angle : 0.451 6.427 29652 Z= 0.232 Chirality : 0.036 0.136 3468 Planarity : 0.004 0.043 3756 Dihedral : 3.475 15.410 2988 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 3.80 % Allowed : 25.69 % Favored : 70.51 % 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: 2.90 (0.16), residues: 2676 helix: 2.73 (0.11), residues: 1824 sheet: 0.16 (0.29), residues: 348 loop : 0.16 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP W 75 HIS 0.001 0.001 HIS N 95 PHE 0.012 0.001 PHE J 77 TYR 0.012 0.001 TYR Q 76 ARG 0.007 0.001 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 260 time to evaluate : 2.469 Fit side-chains REVERT: B 100 PRO cc_start: 0.7947 (Cg_endo) cc_final: 0.7723 (Cg_exo) REVERT: C 17 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7898 (mtmt) REVERT: F 100 PRO cc_start: 0.7919 (Cg_endo) cc_final: 0.7711 (Cg_exo) REVERT: F 115 ARG cc_start: 0.6956 (ttt-90) cc_final: 0.6676 (ttt90) REVERT: G 5 GLU cc_start: 0.7843 (mp0) cc_final: 0.7368 (mm-30) REVERT: H 100 PRO cc_start: 0.7666 (Cg_endo) cc_final: 0.7459 (Cg_exo) REVERT: I 5 GLU cc_start: 0.7754 (mp0) cc_final: 0.7346 (mm-30) REVERT: I 33 LYS cc_start: 0.7485 (mmmm) cc_final: 0.7140 (tptp) REVERT: J 74 ARG cc_start: 0.8363 (ttm170) cc_final: 0.8138 (ttt90) REVERT: J 100 PRO cc_start: 0.7940 (Cg_endo) cc_final: 0.7584 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7737 (mp0) cc_final: 0.7340 (mm-30) REVERT: L 46 LYS cc_start: 0.8712 (ptpp) cc_final: 0.8414 (ptmt) REVERT: N 100 PRO cc_start: 0.7904 (Cg_endo) cc_final: 0.7603 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7716 (mp0) cc_final: 0.7352 (mm-30) REVERT: P 74 ARG cc_start: 0.8430 (ttm170) cc_final: 0.8214 (ttm170) REVERT: Q 5 GLU cc_start: 0.7816 (mp0) cc_final: 0.7332 (mm-30) REVERT: S 5 GLU cc_start: 0.7769 (mp0) cc_final: 0.7403 (mm-30) REVERT: V 100 PRO cc_start: 0.8014 (Cg_endo) cc_final: 0.7626 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7706 (mp0) cc_final: 0.7262 (mm-30) REVERT: W 106 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.8070 (ptpp) outliers start: 83 outliers final: 44 residues processed: 301 average time/residue: 1.8123 time to fit residues: 599.7433 Evaluate side-chains 278 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 232 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 106 LYS Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 190 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.8311 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21804 Z= 0.163 Angle : 0.430 6.887 29652 Z= 0.222 Chirality : 0.035 0.133 3468 Planarity : 0.004 0.065 3756 Dihedral : 3.427 15.187 2988 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.75 % Allowed : 26.37 % Favored : 69.87 % 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: 3.08 (0.16), residues: 2676 helix: 2.87 (0.11), residues: 1824 sheet: 0.15 (0.28), residues: 372 loop : 0.28 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 117 HIS 0.001 0.000 HIS N 95 PHE 0.010 0.001 PHE J 77 TYR 0.013 0.001 TYR Q 76 ARG 0.008 0.001 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 272 time to evaluate : 2.300 Fit side-chains REVERT: A 33 LYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6656 (tptp) REVERT: C 17 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7810 (mtmt) REVERT: D 94 ARG cc_start: 0.8668 (mmm160) cc_final: 0.8285 (mmm-85) REVERT: F 115 ARG cc_start: 0.6959 (ttt-90) cc_final: 0.6660 (ttt90) REVERT: G 5 GLU cc_start: 0.7773 (mp0) cc_final: 0.7320 (mm-30) REVERT: I 5 GLU cc_start: 0.7751 (mp0) cc_final: 0.7351 (mm-30) REVERT: I 33 LYS cc_start: 0.7660 (mmmm) cc_final: 0.7384 (tptp) REVERT: J 51 GLU cc_start: 0.8688 (tt0) cc_final: 0.8455 (tt0) REVERT: J 74 ARG cc_start: 0.8244 (ttm170) cc_final: 0.8028 (ttt90) REVERT: J 100 PRO cc_start: 0.7960 (Cg_endo) cc_final: 0.7605 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7780 (mp0) cc_final: 0.7396 (mm-30) REVERT: L 46 LYS cc_start: 0.8688 (ptpp) cc_final: 0.8443 (ptmt) REVERT: N 100 PRO cc_start: 0.7955 (Cg_endo) cc_final: 0.7615 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7726 (mp0) cc_final: 0.7342 (mm-30) REVERT: Q 5 GLU cc_start: 0.7823 (mp0) cc_final: 0.7394 (mm-30) REVERT: S 5 GLU cc_start: 0.7782 (mp0) cc_final: 0.7413 (mm-30) REVERT: V 92 GLN cc_start: 0.8065 (mt0) cc_final: 0.7777 (mm110) REVERT: V 100 PRO cc_start: 0.7989 (Cg_endo) cc_final: 0.7705 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7737 (mp0) cc_final: 0.7298 (mm-30) REVERT: W 106 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8037 (ptpp) REVERT: X 119 ARG cc_start: 0.6496 (mtm110) cc_final: 0.6175 (mtm110) outliers start: 82 outliers final: 42 residues processed: 315 average time/residue: 1.7982 time to fit residues: 624.5878 Evaluate side-chains 283 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 238 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 121 SER Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 106 LYS Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 55 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.8299 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21804 Z= 0.146 Angle : 0.426 7.383 29652 Z= 0.219 Chirality : 0.035 0.133 3468 Planarity : 0.004 0.070 3756 Dihedral : 3.388 15.306 2988 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 3.16 % Allowed : 27.93 % Favored : 68.91 % 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: 3.24 (0.16), residues: 2676 helix: 2.98 (0.11), residues: 1824 sheet: 0.30 (0.28), residues: 372 loop : 0.32 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP H 117 HIS 0.001 0.000 HIS X 95 PHE 0.011 0.001 PHE B 77 TYR 0.013 0.001 TYR Q 76 ARG 0.008 0.001 ARG V 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 271 time to evaluate : 2.281 Fit side-chains REVERT: A 5 GLU cc_start: 0.7871 (mp0) cc_final: 0.7415 (mm-30) REVERT: A 33 LYS cc_start: 0.6745 (OUTLIER) cc_final: 0.6499 (tptp) REVERT: C 17 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7832 (mtmt) REVERT: D 51 GLU cc_start: 0.8506 (tt0) cc_final: 0.8048 (tt0) REVERT: E 5 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: E 33 LYS cc_start: 0.7867 (mmmm) cc_final: 0.7660 (tptp) REVERT: F 115 ARG cc_start: 0.6987 (ttt-90) cc_final: 0.6693 (ttt90) REVERT: G 5 GLU cc_start: 0.7784 (mp0) cc_final: 0.7312 (mm-30) REVERT: H 74 ARG cc_start: 0.8417 (ttm170) cc_final: 0.8207 (ttm170) REVERT: I 5 GLU cc_start: 0.7635 (mp0) cc_final: 0.7294 (mm-30) REVERT: I 33 LYS cc_start: 0.7717 (mmmm) cc_final: 0.7489 (tptp) REVERT: J 51 GLU cc_start: 0.8667 (tt0) cc_final: 0.8460 (tt0) REVERT: J 100 PRO cc_start: 0.7941 (Cg_endo) cc_final: 0.7603 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7758 (mp0) cc_final: 0.7381 (mm-30) REVERT: L 46 LYS cc_start: 0.8685 (ptpp) cc_final: 0.8431 (ptmt) REVERT: N 100 PRO cc_start: 0.7922 (Cg_endo) cc_final: 0.7590 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7726 (mp0) cc_final: 0.7333 (mm-30) REVERT: Q 5 GLU cc_start: 0.7843 (mp0) cc_final: 0.7404 (mm-30) REVERT: R 51 GLU cc_start: 0.8698 (tt0) cc_final: 0.8480 (tt0) REVERT: S 5 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: V 92 GLN cc_start: 0.8062 (mt0) cc_final: 0.7810 (mm110) REVERT: V 100 PRO cc_start: 0.7931 (Cg_endo) cc_final: 0.7669 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7742 (mp0) cc_final: 0.7293 (mm-30) REVERT: W 106 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7924 (ptpp) outliers start: 69 outliers final: 49 residues processed: 307 average time/residue: 1.7315 time to fit residues: 586.7531 Evaluate side-chains 302 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 248 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 121 SER Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 106 LYS Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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: 0.8336 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21804 Z= 0.223 Angle : 0.471 7.519 29652 Z= 0.237 Chirality : 0.037 0.138 3468 Planarity : 0.004 0.051 3756 Dihedral : 3.469 15.154 2988 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.80 % Allowed : 27.75 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.16), residues: 2676 helix: 2.99 (0.11), residues: 1824 sheet: 0.11 (0.28), residues: 372 loop : 0.38 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 41 HIS 0.002 0.001 HIS X 95 PHE 0.012 0.001 PHE J 77 TYR 0.015 0.001 TYR P 73 ARG 0.009 0.001 ARG H 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 252 time to evaluate : 2.675 Fit side-chains REVERT: A 5 GLU cc_start: 0.7887 (mp0) cc_final: 0.7506 (mm-30) REVERT: A 33 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6829 (tptp) REVERT: C 17 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7920 (mtmt) REVERT: C 33 LYS cc_start: 0.7359 (OUTLIER) cc_final: 0.7048 (mmmm) REVERT: E 5 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: G 5 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: I 5 GLU cc_start: 0.7597 (mp0) cc_final: 0.7305 (mm-30) REVERT: J 51 GLU cc_start: 0.8781 (tt0) cc_final: 0.8571 (tt0) REVERT: J 62 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7633 (ttt-90) REVERT: J 100 PRO cc_start: 0.7968 (Cg_endo) cc_final: 0.7657 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7736 (mp0) cc_final: 0.7335 (mm-30) REVERT: L 46 LYS cc_start: 0.8693 (ptpp) cc_final: 0.8441 (ptmt) REVERT: N 100 PRO cc_start: 0.8057 (Cg_endo) cc_final: 0.7698 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7341 (mm-30) REVERT: Q 5 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: R 62 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7430 (ttt-90) REVERT: S 5 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7513 (mm-30) REVERT: V 92 GLN cc_start: 0.8042 (mt0) cc_final: 0.7711 (mm110) REVERT: V 100 PRO cc_start: 0.7921 (Cg_endo) cc_final: 0.7644 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7365 (mm-30) REVERT: W 32 LEU cc_start: 0.8126 (mm) cc_final: 0.7685 (mp) REVERT: W 106 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8034 (ptpp) outliers start: 83 outliers final: 48 residues processed: 302 average time/residue: 1.4378 time to fit residues: 481.2326 Evaluate side-chains 293 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 233 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 5 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 5 GLU Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 62 ARG Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 121 SER Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 106 LYS Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 231 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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: 0.8364 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 21804 Z= 0.312 Angle : 0.516 7.794 29652 Z= 0.258 Chirality : 0.038 0.136 3468 Planarity : 0.004 0.046 3756 Dihedral : 3.628 14.982 2988 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.80 % Allowed : 28.21 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.16), residues: 2676 helix: 2.88 (0.11), residues: 1824 sheet: -0.08 (0.28), residues: 348 loop : 0.27 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 90 HIS 0.003 0.001 HIS X 95 PHE 0.013 0.001 PHE J 77 TYR 0.017 0.002 TYR P 73 ARG 0.009 0.001 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 244 time to evaluate : 2.584 Fit side-chains REVERT: A 33 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7189 (tptp) REVERT: C 17 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7979 (mtmt) REVERT: D 51 GLU cc_start: 0.8664 (tt0) cc_final: 0.8082 (tt0) REVERT: E 5 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7440 (mm-30) REVERT: G 5 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7289 (mm-30) REVERT: I 5 GLU cc_start: 0.7623 (mp0) cc_final: 0.7324 (mm-30) REVERT: J 100 PRO cc_start: 0.8105 (Cg_endo) cc_final: 0.7734 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7421 (mm-30) REVERT: L 46 LYS cc_start: 0.8748 (ptpp) cc_final: 0.8470 (ptmt) REVERT: N 100 PRO cc_start: 0.8078 (Cg_endo) cc_final: 0.7707 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: P 85 ASP cc_start: 0.7689 (m-30) cc_final: 0.7482 (m-30) REVERT: Q 5 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7447 (mm-30) REVERT: S 5 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7550 (mm-30) REVERT: U 33 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7494 (tptp) REVERT: V 92 GLN cc_start: 0.8027 (mt0) cc_final: 0.7675 (mm110) REVERT: V 100 PRO cc_start: 0.8010 (Cg_endo) cc_final: 0.7719 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7414 (mm-30) REVERT: W 33 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7721 (tptp) REVERT: W 106 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8018 (ptpp) outliers start: 83 outliers final: 47 residues processed: 293 average time/residue: 1.6303 time to fit residues: 529.8157 Evaluate side-chains 286 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 227 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain O residue 5 GLU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 5 GLU Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 121 SER Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 33 LYS Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 106 LYS Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 214 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.8328 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21804 Z= 0.181 Angle : 0.471 8.228 29652 Z= 0.236 Chirality : 0.036 0.136 3468 Planarity : 0.004 0.046 3756 Dihedral : 3.523 15.151 2988 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.93 % Allowed : 29.30 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.16), residues: 2676 helix: 2.99 (0.11), residues: 1824 sheet: -0.05 (0.28), residues: 372 loop : 0.39 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 117 HIS 0.001 0.001 HIS X 95 PHE 0.011 0.001 PHE B 77 TYR 0.014 0.001 TYR X 73 ARG 0.009 0.001 ARG H 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 237 time to evaluate : 2.328 Fit side-chains REVERT: C 5 GLU cc_start: 0.7867 (mp0) cc_final: 0.7554 (mm-30) REVERT: C 17 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7938 (mtmt) REVERT: D 51 GLU cc_start: 0.8592 (tt0) cc_final: 0.8004 (tt0) REVERT: E 5 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7433 (mm-30) REVERT: G 5 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7320 (mm-30) REVERT: I 5 GLU cc_start: 0.7563 (mp0) cc_final: 0.7287 (mm-30) REVERT: J 51 GLU cc_start: 0.8781 (tt0) cc_final: 0.8491 (tt0) REVERT: J 100 PRO cc_start: 0.8110 (Cg_endo) cc_final: 0.7722 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: L 46 LYS cc_start: 0.8642 (ptpp) cc_final: 0.8406 (ptmt) REVERT: N 100 PRO cc_start: 0.8069 (Cg_endo) cc_final: 0.7694 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7753 (mp0) cc_final: 0.7362 (mm-30) REVERT: Q 5 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7451 (mm-30) REVERT: R 51 GLU cc_start: 0.8765 (tt0) cc_final: 0.8480 (tt0) REVERT: S 5 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7513 (mm-30) REVERT: V 100 PRO cc_start: 0.7972 (Cg_endo) cc_final: 0.7614 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7393 (mm-30) REVERT: W 33 LYS cc_start: 0.7732 (mmmm) cc_final: 0.7384 (tptp) REVERT: W 106 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8020 (ptpp) outliers start: 64 outliers final: 46 residues processed: 277 average time/residue: 1.5974 time to fit residues: 492.3786 Evaluate side-chains 282 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 228 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 5 GLU Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 121 SER Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 106 LYS Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 118 optimal weight: 0.0040 chunk 174 optimal weight: 2.9990 chunk 263 optimal weight: 0.4980 chunk 242 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 overall best weight: 0.8794 ------------------------------------------------------------------------------- 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: 0.8305 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21804 Z= 0.150 Angle : 0.458 8.577 29652 Z= 0.229 Chirality : 0.036 0.134 3468 Planarity : 0.004 0.047 3756 Dihedral : 3.424 15.210 2988 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.52 % Allowed : 29.81 % Favored : 67.67 % 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: 3.34 (0.16), residues: 2676 helix: 3.08 (0.11), residues: 1824 sheet: 0.13 (0.28), residues: 372 loop : 0.44 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 117 HIS 0.001 0.000 HIS H 95 PHE 0.010 0.001 PHE B 77 TYR 0.013 0.001 TYR X 73 ARG 0.009 0.001 ARG V 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 236 time to evaluate : 2.405 Fit side-chains REVERT: C 5 GLU cc_start: 0.7850 (mp0) cc_final: 0.7525 (mm-30) REVERT: C 17 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7865 (mtmt) REVERT: E 5 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7425 (mm-30) REVERT: G 5 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: G 33 LYS cc_start: 0.7258 (mptt) cc_final: 0.6888 (tmtm) REVERT: I 5 GLU cc_start: 0.7519 (mp0) cc_final: 0.7280 (mm-30) REVERT: J 51 GLU cc_start: 0.8722 (tt0) cc_final: 0.8451 (tt0) REVERT: J 100 PRO cc_start: 0.8107 (Cg_endo) cc_final: 0.7712 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7347 (mm-30) REVERT: L 46 LYS cc_start: 0.8606 (ptpp) cc_final: 0.8390 (ptmt) REVERT: N 100 PRO cc_start: 0.8036 (Cg_endo) cc_final: 0.7682 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7743 (mp0) cc_final: 0.7348 (mm-30) REVERT: R 51 GLU cc_start: 0.8713 (tt0) cc_final: 0.8434 (tt0) REVERT: S 5 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7542 (mm-30) REVERT: T 100 PRO cc_start: 0.8006 (Cg_endo) cc_final: 0.7647 (Cg_exo) REVERT: V 100 PRO cc_start: 0.7871 (Cg_endo) cc_final: 0.7526 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7390 (mm-30) REVERT: W 106 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7959 (ptpp) REVERT: X 119 ARG cc_start: 0.6625 (mtm110) cc_final: 0.6316 (mtm110) outliers start: 55 outliers final: 44 residues processed: 269 average time/residue: 1.4933 time to fit residues: 450.0401 Evaluate side-chains 279 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 228 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 106 LYS Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 209 optimal weight: 5.9990 chunk 87 optimal weight: 0.0370 chunk 215 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 chunk 184 optimal weight: 0.8980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.136175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117506 restraints weight = 25644.221| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.63 r_work: 0.3279 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 21804 Z= 0.132 Angle : 0.454 8.700 29652 Z= 0.225 Chirality : 0.035 0.139 3468 Planarity : 0.004 0.048 3756 Dihedral : 3.355 15.345 2988 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.20 % Allowed : 30.22 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.49 (0.16), residues: 2676 helix: 3.17 (0.11), residues: 1824 sheet: 0.28 (0.29), residues: 372 loop : 0.49 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP X 117 HIS 0.000 0.000 HIS R 95 PHE 0.010 0.001 PHE B 77 TYR 0.012 0.001 TYR X 73 ARG 0.008 0.001 ARG D 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8203.31 seconds wall clock time: 145 minutes 7.39 seconds (8707.39 seconds total)