Starting phenix.real_space_refine on Sat Sep 28 23:32:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/09_2024/8ump_42381.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/09_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_42381/09_2024/8ump_42381.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/09_2024/8ump_42381.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/09_2024/8ump_42381.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ump_42381/09_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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21432 Number of models: 1 Model: "" Number of chains: 2 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} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, W, D, F, H, J, L, N, P, R, T, V, X Time building chain proxies: 5.85, per 1000 atoms: 0.27 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.31 Conformation dependent library (CDL) restraints added in 2.7 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: 2.11 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: 6.71 Time building geometry restraints manager: 6.17 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: 0.00 - 3.01: 29389 3.01 - 6.01: 191 6.01 - 9.02: 48 9.02 - 12.03: 12 12.03 - 15.03: 12 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: 1.220 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: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 39.710 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.110 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:15.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.510 ------------------------------------------------------------------------------- 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 : 2.478 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: 1.4366 time to fit residues: 422.1190 Evaluate side-chains 226 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 2.364 ------------------------------------------------------------------------------- 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 : 2.285 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: 2.0965 time to fit residues: 762.6830 Evaluate side-chains 242 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 217 time to evaluate : 2.092 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8301 moved from start: 0.1900 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= 0.162 Angle : 0.437 5.439 29652 Z= 0.226 Chirality : 0.035 0.133 3468 Planarity : 0.004 0.044 3756 Dihedral : 3.454 14.619 2988 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.75 % Allowed : 24.59 % Favored : 71.66 % 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: 2.84 (0.16), residues: 2676 helix: 2.62 (0.11), residues: 1824 sheet: 0.56 (0.29), residues: 324 loop : 0.09 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 117 HIS 0.001 0.000 HIS H 95 PHE 0.011 0.001 PHE P 77 TYR 0.015 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 362 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 280 time to evaluate : 2.401 Fit side-chains REVERT: B 100 PRO cc_start: 0.7896 (Cg_endo) cc_final: 0.7629 (Cg_exo) REVERT: E 5 GLU cc_start: 0.7720 (mp0) cc_final: 0.7266 (mm-30) REVERT: F 100 PRO cc_start: 0.7901 (Cg_endo) cc_final: 0.7619 (Cg_exo) REVERT: G 5 GLU cc_start: 0.7750 (mp0) cc_final: 0.7288 (mm-30) REVERT: H 100 PRO cc_start: 0.7684 (Cg_endo) cc_final: 0.7397 (Cg_exo) REVERT: I 5 GLU cc_start: 0.7709 (mp0) cc_final: 0.7471 (mp0) REVERT: J 100 PRO cc_start: 0.7912 (Cg_endo) cc_final: 0.7535 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7713 (mp0) cc_final: 0.7305 (mm-30) REVERT: O 5 GLU cc_start: 0.7718 (mp0) cc_final: 0.7345 (mm-30) REVERT: P 74 ARG cc_start: 0.8384 (ttm170) cc_final: 0.8089 (ttm170) REVERT: P 94 ARG cc_start: 0.8607 (mmm160) cc_final: 0.8386 (mmm-85) REVERT: P 100 PRO cc_start: 0.7703 (Cg_endo) cc_final: 0.7459 (Cg_exo) REVERT: Q 5 GLU cc_start: 0.7799 (mp0) cc_final: 0.7336 (mm-30) REVERT: R 94 ARG cc_start: 0.8599 (mmm160) cc_final: 0.8373 (mmm-85) REVERT: S 5 GLU cc_start: 0.7720 (mp0) cc_final: 0.7270 (mm-30) REVERT: T 94 ARG cc_start: 0.8575 (mmm160) cc_final: 0.8283 (mmm-85) REVERT: V 45 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7814 (pt0) REVERT: V 92 GLN cc_start: 0.8071 (mt0) cc_final: 0.7797 (mm110) REVERT: W 5 GLU cc_start: 0.7719 (mp0) cc_final: 0.7268 (mm-30) REVERT: W 106 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.8035 (ptpp) REVERT: X 100 PRO cc_start: 0.7766 (Cg_endo) cc_final: 0.7516 (Cg_exo) outliers start: 82 outliers final: 22 residues processed: 321 average time/residue: 1.9405 time to fit residues: 681.3522 Evaluate side-chains 241 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 217 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP 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 G residue 46 GLU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain L residue 45 GLU 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 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: 2.9990 chunk 180 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 chunk 241 optimal weight: 7.9990 chunk 255 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.8320 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21804 Z= 0.191 Angle : 0.442 6.636 29652 Z= 0.228 Chirality : 0.036 0.135 3468 Planarity : 0.004 0.043 3756 Dihedral : 3.455 15.543 2988 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 3.34 % Allowed : 26.14 % 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: 2.99 (0.16), residues: 2676 helix: 2.78 (0.11), residues: 1824 sheet: 0.18 (0.28), residues: 372 loop : 0.27 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 117 HIS 0.001 0.001 HIS N 95 PHE 0.012 0.001 PHE J 77 TYR 0.013 0.001 TYR Q 76 ARG 0.010 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 342 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 269 time to evaluate : 2.262 Fit side-chains REVERT: B 100 PRO cc_start: 0.7937 (Cg_endo) cc_final: 0.7721 (Cg_exo) REVERT: C 17 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7839 (mtmt) REVERT: F 115 ARG cc_start: 0.6963 (ttt-90) cc_final: 0.6693 (ttt90) REVERT: G 5 GLU cc_start: 0.7850 (mp0) cc_final: 0.7368 (mm-30) REVERT: H 100 PRO cc_start: 0.7634 (Cg_endo) cc_final: 0.7430 (Cg_exo) REVERT: I 5 GLU cc_start: 0.7719 (mp0) cc_final: 0.7274 (mm-30) REVERT: I 33 LYS cc_start: 0.7465 (mmmm) cc_final: 0.7165 (tptp) REVERT: J 100 PRO cc_start: 0.7925 (Cg_endo) cc_final: 0.7555 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7739 (mp0) cc_final: 0.7337 (mm-30) REVERT: L 46 LYS cc_start: 0.8702 (ptpp) cc_final: 0.8419 (ptmt) REVERT: N 100 PRO cc_start: 0.7931 (Cg_endo) cc_final: 0.7605 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7705 (mp0) cc_final: 0.7340 (mm-30) REVERT: P 74 ARG cc_start: 0.8421 (ttm170) cc_final: 0.8209 (ttm170) REVERT: Q 5 GLU cc_start: 0.7816 (mp0) cc_final: 0.7335 (mm-30) REVERT: S 5 GLU cc_start: 0.7787 (mp0) cc_final: 0.7407 (mm-30) REVERT: V 45 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: V 100 PRO cc_start: 0.7975 (Cg_endo) cc_final: 0.7591 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7716 (mp0) cc_final: 0.7275 (mm-30) REVERT: W 106 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.8043 (ptpp) REVERT: X 74 ARG cc_start: 0.8477 (ttm170) cc_final: 0.8236 (ttm170) REVERT: X 119 ARG cc_start: 0.6391 (mtm110) cc_final: 0.6186 (mtm110) outliers start: 73 outliers final: 34 residues processed: 303 average time/residue: 1.7851 time to fit residues: 594.7921 Evaluate side-chains 281 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 244 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 17 LYS 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 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 55 THR 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 M residue 89 ASP Chi-restraints excluded: chain M residue 107 THR 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 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 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 Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 55 THR 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: 0.9990 chunk 3 optimal weight: 0.8980 chunk 190 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 229 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.8298 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21804 Z= 0.147 Angle : 0.422 6.862 29652 Z= 0.218 Chirality : 0.035 0.133 3468 Planarity : 0.004 0.066 3756 Dihedral : 3.386 15.241 2988 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.71 % Allowed : 26.65 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.16), residues: 2676 helix: 2.93 (0.11), residues: 1824 sheet: 0.27 (0.28), residues: 372 loop : 0.29 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 117 HIS 0.001 0.000 HIS N 95 PHE 0.010 0.001 PHE D 77 TYR 0.013 0.001 TYR M 76 ARG 0.009 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 360 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 279 time to evaluate : 2.071 Fit side-chains REVERT: A 5 GLU cc_start: 0.7856 (mp0) cc_final: 0.7431 (mm-30) REVERT: A 33 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6528 (tptp) REVERT: C 17 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7801 (mtmt) REVERT: D 94 ARG cc_start: 0.8661 (mmm160) cc_final: 0.8284 (mmm-85) REVERT: F 115 ARG cc_start: 0.6952 (ttt-90) cc_final: 0.6670 (ttt90) REVERT: G 5 GLU cc_start: 0.7769 (mp0) cc_final: 0.7293 (mm-30) REVERT: I 5 GLU cc_start: 0.7718 (mp0) cc_final: 0.7317 (mm-30) REVERT: I 33 LYS cc_start: 0.7651 (mmmm) cc_final: 0.7376 (tptp) REVERT: J 100 PRO cc_start: 0.7947 (Cg_endo) cc_final: 0.7598 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7714 (mp0) cc_final: 0.7301 (mm-30) REVERT: L 46 LYS cc_start: 0.8708 (ptpp) cc_final: 0.8482 (ptmt) REVERT: N 100 PRO cc_start: 0.7948 (Cg_endo) cc_final: 0.7603 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7730 (mp0) cc_final: 0.7342 (mm-30) REVERT: P 74 ARG cc_start: 0.8377 (ttm170) cc_final: 0.8132 (ttt90) REVERT: Q 5 GLU cc_start: 0.7839 (mp0) cc_final: 0.7370 (mm-30) REVERT: R 51 GLU cc_start: 0.8707 (tt0) cc_final: 0.8488 (tt0) REVERT: S 5 GLU cc_start: 0.7778 (mp0) cc_final: 0.7405 (mm-30) REVERT: V 92 GLN cc_start: 0.8042 (mt0) cc_final: 0.7768 (mm110) REVERT: V 100 PRO cc_start: 0.7945 (Cg_endo) cc_final: 0.7669 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7729 (mp0) cc_final: 0.7283 (mm-30) REVERT: W 106 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7936 (ptpp) REVERT: X 119 ARG cc_start: 0.6466 (mtm110) cc_final: 0.6228 (mtm110) outliers start: 81 outliers final: 46 residues processed: 322 average time/residue: 1.8613 time to fit residues: 658.4236 Evaluate side-chains 289 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 240 time to evaluate : 2.276 ------------------------------------------------------------------------------- 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 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 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 46 GLU Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 70 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 89 ASP Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 70 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 4.9990 chunk 229 optimal weight: 4.9990 chunk 50 optimal weight: 0.2980 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 255 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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: 0.8291 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21804 Z= 0.143 Angle : 0.429 7.354 29652 Z= 0.219 Chirality : 0.035 0.132 3468 Planarity : 0.004 0.067 3756 Dihedral : 3.361 15.358 2988 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.07 % Allowed : 28.07 % Favored : 68.86 % 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: 3.33 (0.16), residues: 2676 helix: 3.03 (0.11), residues: 1824 sheet: 0.41 (0.29), residues: 372 loop : 0.35 (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 0.009 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 331 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 264 time to evaluate : 2.346 Fit side-chains REVERT: A 5 GLU cc_start: 0.7844 (mp0) cc_final: 0.7412 (mm-30) REVERT: A 33 LYS cc_start: 0.6794 (OUTLIER) cc_final: 0.6402 (tptp) REVERT: B 51 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8613 (tm-30) REVERT: C 17 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7824 (mtmt) REVERT: D 51 GLU cc_start: 0.8443 (tt0) cc_final: 0.7978 (tt0) REVERT: E 5 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7411 (mm-30) REVERT: E 33 LYS cc_start: 0.7851 (mmmm) cc_final: 0.7641 (tptp) REVERT: F 115 ARG cc_start: 0.6974 (ttt-90) cc_final: 0.6694 (ttt90) REVERT: G 5 GLU cc_start: 0.7784 (mp0) cc_final: 0.7306 (mm-30) REVERT: I 5 GLU cc_start: 0.7633 (mp0) cc_final: 0.7291 (mm-30) REVERT: I 33 LYS cc_start: 0.7715 (mmmm) cc_final: 0.7476 (tptp) REVERT: J 51 GLU cc_start: 0.8815 (tt0) cc_final: 0.8599 (tt0) REVERT: J 100 PRO cc_start: 0.8006 (Cg_endo) cc_final: 0.7660 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7771 (mp0) cc_final: 0.7372 (mm-30) REVERT: L 46 LYS cc_start: 0.8679 (ptpp) cc_final: 0.8453 (ptmt) REVERT: N 100 PRO cc_start: 0.7933 (Cg_endo) cc_final: 0.7602 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7734 (mp0) cc_final: 0.7303 (mm-30) REVERT: Q 5 GLU cc_start: 0.7838 (mp0) cc_final: 0.7398 (mm-30) REVERT: R 100 PRO cc_start: 0.7790 (Cg_endo) cc_final: 0.7446 (Cg_exo) REVERT: S 5 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7413 (mm-30) REVERT: U 32 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7873 (mp) REVERT: V 92 GLN cc_start: 0.8047 (mt0) cc_final: 0.7823 (mm110) REVERT: V 100 PRO cc_start: 0.7825 (Cg_endo) cc_final: 0.7590 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7739 (mp0) cc_final: 0.7297 (mm-30) REVERT: W 106 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7914 (ptpp) REVERT: X 119 ARG cc_start: 0.6474 (mtm110) cc_final: 0.6234 (mtm110) outliers start: 67 outliers final: 40 residues processed: 296 average time/residue: 1.7459 time to fit residues: 572.4030 Evaluate side-chains 289 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 243 time to evaluate : 2.222 ------------------------------------------------------------------------------- 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 106 THR 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 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 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 89 ASP Chi-restraints excluded: chain P residue 45 GLU 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 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 32 LEU 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 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: 3.9990 chunk 28 optimal weight: 0.9980 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: 3.9990 chunk 254 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.8341 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 21804 Z= 0.247 Angle : 0.480 7.522 29652 Z= 0.242 Chirality : 0.037 0.136 3468 Planarity : 0.004 0.050 3756 Dihedral : 3.486 14.916 2988 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.62 % Allowed : 27.98 % Favored : 68.41 % 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: 3.23 (0.16), residues: 2676 helix: 3.00 (0.11), residues: 1824 sheet: 0.20 (0.29), residues: 348 loop : 0.28 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 90 HIS 0.002 0.001 HIS X 95 PHE 0.012 0.001 PHE J 77 TYR 0.016 0.002 TYR P 73 ARG 0.008 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 324 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 245 time to evaluate : 3.631 Fit side-chains REVERT: A 5 GLU cc_start: 0.7914 (mp0) cc_final: 0.7522 (mm-30) REVERT: A 33 LYS cc_start: 0.7331 (mptt) cc_final: 0.6964 (tptp) REVERT: C 17 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7914 (mtmt) REVERT: C 33 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.7043 (mmmm) REVERT: E 5 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7408 (mm-30) REVERT: E 33 LYS cc_start: 0.7953 (mmmm) cc_final: 0.7750 (tptp) REVERT: G 5 GLU cc_start: 0.7794 (mp0) cc_final: 0.7343 (mm-30) REVERT: I 5 GLU cc_start: 0.7606 (mp0) cc_final: 0.7309 (mm-30) REVERT: I 33 LYS cc_start: 0.7808 (mmmm) cc_final: 0.7607 (tptp) REVERT: J 62 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7635 (ttt-90) REVERT: J 100 PRO cc_start: 0.8096 (Cg_endo) cc_final: 0.7704 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7773 (mp0) cc_final: 0.7390 (mm-30) REVERT: L 46 LYS cc_start: 0.8704 (ptpp) cc_final: 0.8463 (ptmt) REVERT: N 100 PRO cc_start: 0.8071 (Cg_endo) cc_final: 0.7711 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7749 (mp0) cc_final: 0.7365 (mm-30) REVERT: Q 5 GLU cc_start: 0.7806 (mp0) cc_final: 0.7382 (mm-30) REVERT: R 62 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7437 (ttt-90) REVERT: S 5 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7509 (mm-30) REVERT: U 32 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7972 (mp) REVERT: V 92 GLN cc_start: 0.8052 (mt0) cc_final: 0.7703 (mm110) REVERT: V 100 PRO cc_start: 0.7912 (Cg_endo) cc_final: 0.7640 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7368 (mm-30) REVERT: W 106 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8030 (ptpp) REVERT: X 119 ARG cc_start: 0.6529 (mtm110) cc_final: 0.6255 (mtm110) outliers start: 79 outliers final: 48 residues processed: 293 average time/residue: 1.5448 time to fit residues: 502.4037 Evaluate side-chains 288 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 231 time to evaluate : 2.285 ------------------------------------------------------------------------------- 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 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 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 46 GLU 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 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 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 55 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 106 LYS 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: 3.9990 chunk 101 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8314 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21804 Z= 0.168 Angle : 0.459 7.966 29652 Z= 0.229 Chirality : 0.036 0.136 3468 Planarity : 0.004 0.046 3756 Dihedral : 3.429 14.984 2988 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.34 % Allowed : 28.66 % 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: 3.35 (0.16), residues: 2676 helix: 3.07 (0.11), residues: 1824 sheet: 0.21 (0.28), residues: 372 loop : 0.46 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP N 90 HIS 0.001 0.001 HIS H 95 PHE 0.011 0.001 PHE B 77 TYR 0.014 0.001 TYR P 73 ARG 0.008 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 318 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 245 time to evaluate : 2.502 Fit side-chains REVERT: A 33 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6657 (tptp) REVERT: B 73 TYR cc_start: 0.8703 (m-80) cc_final: 0.8471 (m-80) REVERT: C 17 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7852 (mtmt) REVERT: D 51 GLU cc_start: 0.8530 (tt0) cc_final: 0.7905 (tt0) REVERT: E 5 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7447 (mm-30) REVERT: G 5 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7311 (mm-30) REVERT: I 5 GLU cc_start: 0.7547 (mp0) cc_final: 0.7298 (mm-30) REVERT: I 33 LYS cc_start: 0.7841 (mmmm) cc_final: 0.7490 (tptp) REVERT: J 51 GLU cc_start: 0.8844 (tt0) cc_final: 0.8630 (tt0) REVERT: J 62 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7644 (ttt-90) REVERT: J 100 PRO cc_start: 0.8095 (Cg_endo) cc_final: 0.7700 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7399 (mm-30) REVERT: L 46 LYS cc_start: 0.8644 (ptpp) cc_final: 0.8427 (ptmt) REVERT: N 100 PRO cc_start: 0.7998 (Cg_endo) cc_final: 0.7656 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7730 (mp0) cc_final: 0.7332 (mm-30) REVERT: Q 5 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7393 (mm-30) REVERT: R 51 GLU cc_start: 0.8742 (tt0) cc_final: 0.8502 (tt0) REVERT: R 62 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7467 (ttt-90) REVERT: R 100 PRO cc_start: 0.7819 (Cg_endo) cc_final: 0.7491 (Cg_exo) REVERT: S 5 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: T 100 PRO cc_start: 0.8041 (Cg_endo) cc_final: 0.7682 (Cg_exo) REVERT: U 32 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7982 (mp) REVERT: V 92 GLN cc_start: 0.8031 (mt0) cc_final: 0.7763 (mm110) REVERT: V 100 PRO cc_start: 0.7921 (Cg_endo) cc_final: 0.7666 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7354 (mm-30) REVERT: W 106 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7969 (ptpp) REVERT: X 119 ARG cc_start: 0.6560 (mtm110) cc_final: 0.6233 (mtm110) outliers start: 73 outliers final: 44 residues processed: 285 average time/residue: 1.6056 time to fit residues: 508.3136 Evaluate side-chains 290 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 234 time to evaluate : 2.256 ------------------------------------------------------------------------------- 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 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 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 I residue 46 GLU Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 62 ARG 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 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 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 32 LEU 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 5 GLU 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 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: 5.9990 chunk 222 optimal weight: 0.8980 chunk 237 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 186 optimal weight: 0.0870 chunk 72 optimal weight: 0.4980 chunk 214 optimal weight: 0.8980 chunk 224 optimal weight: 7.9990 chunk 236 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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: 0.8279 moved from start: 0.2571 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= 0.135 Angle : 0.446 8.547 29652 Z= 0.221 Chirality : 0.035 0.135 3468 Planarity : 0.004 0.047 3756 Dihedral : 3.332 15.081 2988 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.52 % Allowed : 29.72 % 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: 3.52 (0.16), residues: 2676 helix: 3.16 (0.11), residues: 1824 sheet: 0.41 (0.29), residues: 372 loop : 0.51 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP V 117 HIS 0.001 0.000 HIS H 95 PHE 0.009 0.001 PHE B 77 TYR 0.012 0.001 TYR M 76 ARG 0.008 0.001 ARG V 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 303 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 248 time to evaluate : 2.399 Fit side-chains REVERT: A 5 GLU cc_start: 0.7862 (mp0) cc_final: 0.7441 (mm-30) REVERT: B 73 TYR cc_start: 0.8618 (m-80) cc_final: 0.8416 (m-80) REVERT: C 5 GLU cc_start: 0.7817 (mp0) cc_final: 0.7442 (mm-30) REVERT: C 17 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7848 (mtmt) REVERT: D 51 GLU cc_start: 0.8379 (tt0) cc_final: 0.7782 (tt0) REVERT: E 5 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7427 (mm-30) REVERT: G 5 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7332 (mm-30) REVERT: I 5 GLU cc_start: 0.7486 (mp0) cc_final: 0.7248 (mm-30) REVERT: I 33 LYS cc_start: 0.7855 (mmmm) cc_final: 0.7522 (tptp) REVERT: J 51 GLU cc_start: 0.8790 (tt0) cc_final: 0.8534 (tt0) REVERT: J 62 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7625 (ttt-90) REVERT: J 100 PRO cc_start: 0.8082 (Cg_endo) cc_final: 0.7691 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7806 (mp0) cc_final: 0.7412 (mm-30) REVERT: N 100 PRO cc_start: 0.7948 (Cg_endo) cc_final: 0.7626 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7708 (mp0) cc_final: 0.7297 (mm-30) REVERT: Q 5 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: R 51 GLU cc_start: 0.8624 (tt0) cc_final: 0.8406 (tt0) REVERT: R 62 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7474 (ttt-90) REVERT: R 100 PRO cc_start: 0.7818 (Cg_endo) cc_final: 0.7521 (Cg_exo) REVERT: T 100 PRO cc_start: 0.7976 (Cg_endo) cc_final: 0.7628 (Cg_exo) REVERT: U 32 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8015 (mp) REVERT: V 92 GLN cc_start: 0.8000 (mt0) cc_final: 0.7754 (mm110) REVERT: V 100 PRO cc_start: 0.7884 (Cg_endo) cc_final: 0.7645 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7352 (mm-30) REVERT: W 106 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7908 (ptpp) REVERT: X 115 ARG cc_start: 0.7019 (ttt-90) cc_final: 0.6764 (ttt-90) REVERT: X 119 ARG cc_start: 0.6516 (mtm110) cc_final: 0.6218 (mtm110) outliers start: 55 outliers final: 29 residues processed: 275 average time/residue: 1.5842 time to fit residues: 489.0512 Evaluate side-chains 275 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 237 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 89 ASP 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 I residue 46 GLU Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 62 ARG 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 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 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 89 ASP Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 32 LEU 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 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: 0.0970 chunk 153 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 174 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.8291 moved from start: 0.2573 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= 0.152 Angle : 0.453 8.558 29652 Z= 0.226 Chirality : 0.036 0.134 3468 Planarity : 0.004 0.047 3756 Dihedral : 3.348 15.083 2988 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.38 % Allowed : 29.81 % Favored : 67.81 % 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: 3.54 (0.16), residues: 2676 helix: 3.17 (0.11), residues: 1824 sheet: 0.41 (0.29), residues: 372 loop : 0.56 (0.32), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP P 117 HIS 0.001 0.000 HIS X 95 PHE 0.012 0.001 PHE B 77 TYR 0.014 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 292 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 240 time to evaluate : 2.335 Fit side-chains REVERT: A 5 GLU cc_start: 0.7879 (mp0) cc_final: 0.7439 (mm-30) REVERT: A 33 LYS cc_start: 0.7195 (mptt) cc_final: 0.6914 (tptp) REVERT: C 5 GLU cc_start: 0.7829 (mp0) cc_final: 0.7463 (mm-30) REVERT: C 17 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7865 (mtmt) REVERT: D 51 GLU cc_start: 0.8456 (tt0) cc_final: 0.7864 (tt0) REVERT: E 5 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7452 (mm-30) REVERT: G 5 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7330 (mm-30) REVERT: I 5 GLU cc_start: 0.7493 (mp0) cc_final: 0.7249 (mm-30) REVERT: I 33 LYS cc_start: 0.7878 (mmmm) cc_final: 0.7569 (tptp) REVERT: J 51 GLU cc_start: 0.8805 (tt0) cc_final: 0.8604 (tt0) REVERT: J 62 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7594 (ttt-90) REVERT: J 100 PRO cc_start: 0.8091 (Cg_endo) cc_final: 0.7704 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7417 (mm-30) REVERT: L 100 PRO cc_start: 0.7873 (Cg_endo) cc_final: 0.7530 (Cg_exo) REVERT: N 100 PRO cc_start: 0.7871 (Cg_endo) cc_final: 0.7585 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7724 (mp0) cc_final: 0.7285 (mm-30) REVERT: Q 5 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: R 51 GLU cc_start: 0.8672 (tt0) cc_final: 0.8448 (tt0) REVERT: R 62 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7437 (ttt-90) REVERT: R 100 PRO cc_start: 0.7728 (Cg_endo) cc_final: 0.7448 (Cg_exo) REVERT: T 100 PRO cc_start: 0.7982 (Cg_endo) cc_final: 0.7643 (Cg_exo) REVERT: U 32 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8052 (mp) REVERT: V 51 GLU cc_start: 0.8338 (tp30) cc_final: 0.7761 (tm-30) REVERT: V 92 GLN cc_start: 0.8029 (mt0) cc_final: 0.7793 (mm110) REVERT: V 100 PRO cc_start: 0.7888 (Cg_endo) cc_final: 0.7642 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: W 106 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7911 (ptpp) outliers start: 52 outliers final: 34 residues processed: 267 average time/residue: 1.5105 time to fit residues: 450.9108 Evaluate side-chains 277 residues out of total 2184 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 233 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 106 THR 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 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 106 THR Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 62 ARG 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 O residue 89 ASP Chi-restraints excluded: chain P residue 45 GLU 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 89 ASP Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 32 LEU 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 106 LYS Chi-restraints excluded: chain X residue 55 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.0070 chunk 64 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 209 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 184 optimal weight: 0.2980 overall best weight: 2.0604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.112854 restraints weight = 25930.004| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.64 r_work: 0.3208 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21804 Z= 0.237 Angle : 0.501 8.327 29652 Z= 0.248 Chirality : 0.037 0.138 3468 Planarity : 0.004 0.046 3756 Dihedral : 3.497 14.885 2988 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.84 % Allowed : 29.62 % Favored : 67.54 % 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: 3.37 (0.16), residues: 2676 helix: 3.08 (0.11), residues: 1824 sheet: 0.28 (0.29), residues: 348 loop : 0.42 (0.31), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP N 90 HIS 0.002 0.001 HIS X 95 PHE 0.013 0.001 PHE B 77 TYR 0.018 0.002 TYR H 73 ARG 0.009 0.001 ARG V 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8214.48 seconds wall clock time: 143 minutes 58.98 seconds (8638.98 seconds total)