Starting phenix.real_space_refine on Sun Aug 24 14:54:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ump_42381/08_2025/8ump_42381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ump_42381/08_2025/8ump_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/cci-nas-00/data/ceres_data/8ump_42381/08_2025/8ump_42381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ump_42381/08_2025/8ump_42381.map" model { file = "/net/cci-nas-00/data/ceres_data/8ump_42381/08_2025/8ump_42381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ump_42381/08_2025/8ump_42381.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.89, per 1000 atoms: 0.09 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: 1.94 Conformation dependent library (CDL) restraints added in 929.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.56 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: 4.09 Time building geometry restraints manager: 2.52 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: 0.08 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.600 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.860 ------------------------------------------------------------------------------- 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= 0.238 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG P 115 TYR 0.016 0.002 TYR X 73 PHE 0.008 0.001 PHE D 77 TRP 0.002 0.001 TRP D 90 HIS 0.002 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00670 (21804) covalent geometry : angle 0.73597 (29652) hydrogen bonds : bond 0.19611 ( 1632) hydrogen bonds : angle 6.11215 ( 4824) *********************** 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 to be fit. rotamer outliers: 15 poor density : 260 time to evaluate : 0.645 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: 0.6160 time to fit residues: 181.2263 Evaluate side-chains 226 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.111697 restraints weight = 25867.615| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.66 r_work: 0.3192 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21804 Z= 0.158 Angle : 0.505 5.197 29652 Z= 0.261 Chirality : 0.037 0.130 3468 Planarity : 0.004 0.042 3756 Dihedral : 3.795 26.401 2992 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 3.98 % Allowed : 23.95 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.16), residues: 2676 helix: 2.14 (0.11), residues: 1824 sheet: -0.44 (0.26), residues: 348 loop : 0.34 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 115 TYR 0.015 0.002 TYR Q 27 PHE 0.013 0.002 PHE J 77 TRP 0.004 0.001 TRP I 75 HIS 0.002 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00400 (21804) covalent geometry : angle 0.50518 (29652) hydrogen bonds : bond 0.04261 ( 1632) hydrogen bonds : angle 3.89839 ( 4824) *********************** 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 377 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 290 time to evaluate : 0.812 Fit side-chains REVERT: B 73 TYR cc_start: 0.8875 (m-80) cc_final: 0.8659 (m-80) REVERT: B 74 ARG cc_start: 0.8488 (ttm170) cc_final: 0.8253 (ttm170) REVERT: B 94 ARG cc_start: 0.8627 (mmm160) cc_final: 0.8355 (mmm-85) REVERT: F 100 PRO cc_start: 0.8124 (Cg_endo) cc_final: 0.7764 (Cg_exo) REVERT: G 5 GLU cc_start: 0.8019 (mp0) cc_final: 0.7447 (mm-30) REVERT: H 100 PRO cc_start: 0.7986 (Cg_endo) cc_final: 0.7636 (Cg_exo) REVERT: J 94 ARG cc_start: 0.8656 (mmm160) cc_final: 0.8362 (mmm-85) REVERT: K 5 GLU cc_start: 0.8054 (mp0) cc_final: 0.7523 (mm-30) REVERT: N 115 ARG cc_start: 0.7243 (ttt-90) cc_final: 0.6844 (ttt-90) REVERT: N 119 ARG cc_start: 0.7046 (mtm180) cc_final: 0.6840 (mtm110) REVERT: O 5 GLU cc_start: 0.7971 (mp0) cc_final: 0.7511 (mm-30) REVERT: P 81 ARG cc_start: 0.8364 (ptp90) cc_final: 0.8157 (ptt-90) REVERT: P 100 PRO cc_start: 0.8069 (Cg_endo) cc_final: 0.7741 (Cg_exo) REVERT: V 92 GLN cc_start: 0.8345 (mt0) cc_final: 0.8119 (mm110) REVERT: X 62 ARG cc_start: 0.8354 (mtt-85) cc_final: 0.8063 (ttt180) REVERT: X 100 PRO cc_start: 0.8002 (Cg_endo) cc_final: 0.7668 (Cg_exo) outliers start: 87 outliers final: 25 residues processed: 324 average time/residue: 0.8845 time to fit residues: 312.0444 Evaluate side-chains 247 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 107 THR 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 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 S residue 107 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 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 110 optimal weight: 10.0000 chunk 232 optimal weight: 0.9990 chunk 250 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 256 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.131349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112315 restraints weight = 25826.722| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.66 r_work: 0.3209 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21804 Z= 0.132 Angle : 0.459 5.414 29652 Z= 0.237 Chirality : 0.036 0.133 3468 Planarity : 0.004 0.045 3756 Dihedral : 3.548 14.667 2988 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.26 % Allowed : 25.64 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.16), residues: 2676 helix: 2.53 (0.11), residues: 1824 sheet: -0.12 (0.27), residues: 348 loop : 0.20 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 61 TYR 0.014 0.001 TYR I 76 PHE 0.012 0.001 PHE P 77 TRP 0.003 0.001 TRP W 75 HIS 0.001 0.001 HIS T 95 Details of bonding type rmsd covalent geometry : bond 0.00324 (21804) covalent geometry : angle 0.45920 (29652) hydrogen bonds : bond 0.03663 ( 1632) hydrogen bonds : angle 3.61387 ( 4824) *********************** 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 353 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 260 time to evaluate : 0.874 Fit side-chains REVERT: B 73 TYR cc_start: 0.8801 (m-80) cc_final: 0.8580 (m-80) REVERT: F 100 PRO cc_start: 0.8154 (Cg_endo) cc_final: 0.7873 (Cg_exo) REVERT: G 5 GLU cc_start: 0.8042 (mp0) cc_final: 0.7499 (mm-30) REVERT: H 74 ARG cc_start: 0.8400 (ttm170) cc_final: 0.8183 (ttm170) REVERT: H 100 PRO cc_start: 0.7996 (Cg_endo) cc_final: 0.7740 (Cg_exo) REVERT: J 100 PRO cc_start: 0.8129 (Cg_endo) cc_final: 0.7774 (Cg_exo) REVERT: K 5 GLU cc_start: 0.8078 (mp0) cc_final: 0.7584 (mm-30) REVERT: M 33 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7044 (mmmm) REVERT: O 5 GLU cc_start: 0.8040 (mp0) cc_final: 0.7606 (mm-30) REVERT: P 81 ARG cc_start: 0.8348 (ptp90) cc_final: 0.8142 (ptt-90) REVERT: P 100 PRO cc_start: 0.7969 (Cg_endo) cc_final: 0.7731 (Cg_exo) REVERT: W 106 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8059 (ptpp) REVERT: X 62 ARG cc_start: 0.8416 (mtt-85) cc_final: 0.8174 (ttt180) REVERT: X 100 PRO cc_start: 0.7987 (Cg_endo) cc_final: 0.7745 (Cg_exo) outliers start: 93 outliers final: 34 residues processed: 310 average time/residue: 0.7591 time to fit residues: 258.9542 Evaluate side-chains 245 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 32 THR Chi-restraints excluded: chain D residue 106 THR 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 46 GLU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 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 55 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 106 LYS Chi-restraints excluded: chain X residue 55 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 174 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.127696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108707 restraints weight = 26048.111| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.64 r_work: 0.3151 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21804 Z= 0.218 Angle : 0.516 6.252 29652 Z= 0.262 Chirality : 0.039 0.138 3468 Planarity : 0.004 0.046 3756 Dihedral : 3.692 15.231 2988 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.67 % Allowed : 25.14 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.16), residues: 2676 helix: 2.51 (0.11), residues: 1824 sheet: -0.30 (0.27), residues: 348 loop : 0.08 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 115 TYR 0.014 0.002 TYR P 73 PHE 0.014 0.002 PHE J 77 TRP 0.003 0.001 TRP A 41 HIS 0.002 0.002 HIS R 95 Details of bonding type rmsd covalent geometry : bond 0.00546 (21804) covalent geometry : angle 0.51650 (29652) hydrogen bonds : bond 0.04029 ( 1632) hydrogen bonds : angle 3.69493 ( 4824) *********************** 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 358 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 256 time to evaluate : 0.841 Fit side-chains REVERT: B 51 GLU cc_start: 0.8975 (tt0) cc_final: 0.8770 (tt0) REVERT: C 17 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8106 (mtmt) REVERT: F 100 PRO cc_start: 0.8218 (Cg_endo) cc_final: 0.8005 (Cg_exo) REVERT: G 33 LYS cc_start: 0.7709 (mptt) cc_final: 0.7264 (mmmm) REVERT: H 100 PRO cc_start: 0.8072 (Cg_endo) cc_final: 0.7847 (Cg_exo) REVERT: K 5 GLU cc_start: 0.8077 (mp0) cc_final: 0.7627 (mm-30) REVERT: P 119 ARG cc_start: 0.7049 (mtm110) cc_final: 0.6775 (mtp180) REVERT: V 92 GLN cc_start: 0.8276 (mt0) cc_final: 0.8020 (mm110) REVERT: W 106 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8030 (ptpp) outliers start: 102 outliers final: 55 residues processed: 315 average time/residue: 0.7553 time to fit residues: 262.1737 Evaluate side-chains 290 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 233 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 107 THR 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 C residue 107 THR Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 89 ASP 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 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 N residue 121 SER Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain S residue 107 THR 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 89 ASP Chi-restraints excluded: chain U residue 106 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 251 optimal weight: 0.9980 chunk 263 optimal weight: 9.9990 chunk 233 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.132463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113668 restraints weight = 25835.918| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.64 r_work: 0.3209 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2265 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= 0.103 Angle : 0.429 6.866 29652 Z= 0.223 Chirality : 0.035 0.134 3468 Planarity : 0.004 0.062 3756 Dihedral : 3.506 15.250 2988 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.75 % Allowed : 26.74 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.87 (0.16), residues: 2676 helix: 2.78 (0.11), residues: 1824 sheet: -0.05 (0.28), residues: 348 loop : 0.01 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 115 TYR 0.014 0.001 TYR U 76 PHE 0.011 0.001 PHE P 77 TRP 0.003 0.001 TRP P 117 HIS 0.001 0.000 HIS X 95 Details of bonding type rmsd covalent geometry : bond 0.00244 (21804) covalent geometry : angle 0.42902 (29652) hydrogen bonds : bond 0.03175 ( 1632) hydrogen bonds : angle 3.43109 ( 4824) *********************** 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 351 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 269 time to evaluate : 0.872 Fit side-chains REVERT: A 5 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7503 (mm-30) REVERT: B 73 TYR cc_start: 0.8790 (m-80) cc_final: 0.8507 (m-80) REVERT: C 17 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7859 (mtmt) REVERT: E 5 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7610 (mm-30) REVERT: F 100 PRO cc_start: 0.8121 (Cg_endo) cc_final: 0.7910 (Cg_exo) REVERT: G 33 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7206 (mmmm) REVERT: I 5 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7652 (mm-30) REVERT: J 100 PRO cc_start: 0.8152 (Cg_endo) cc_final: 0.7790 (Cg_exo) REVERT: K 5 GLU cc_start: 0.8062 (mp0) cc_final: 0.7566 (mm-30) REVERT: M 33 LYS cc_start: 0.7632 (mptt) cc_final: 0.7229 (mmmm) REVERT: N 100 PRO cc_start: 0.8011 (Cg_endo) cc_final: 0.7740 (Cg_exo) REVERT: U 33 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7444 (tptp) REVERT: V 92 GLN cc_start: 0.8211 (mt0) cc_final: 0.8010 (mm110) REVERT: V 100 PRO cc_start: 0.8173 (Cg_endo) cc_final: 0.7899 (Cg_exo) REVERT: W 106 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7945 (ptpp) REVERT: X 119 ARG cc_start: 0.6933 (mtm110) cc_final: 0.6719 (mtm110) outliers start: 82 outliers final: 37 residues processed: 316 average time/residue: 0.7796 time to fit residues: 270.8735 Evaluate side-chains 281 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 32 THR 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 F residue 45 GLU Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain G residue 33 LYS 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 5 GLU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain 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 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 22 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 33 LYS 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 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 247 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 249 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.133938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115209 restraints weight = 25631.238| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.63 r_work: 0.3240 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21804 Z= 0.097 Angle : 0.421 7.520 29652 Z= 0.218 Chirality : 0.035 0.134 3468 Planarity : 0.004 0.065 3756 Dihedral : 3.398 15.131 2988 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.48 % Allowed : 27.56 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.15 (0.16), residues: 2676 helix: 2.96 (0.11), residues: 1824 sheet: 0.22 (0.29), residues: 348 loop : 0.08 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 61 TYR 0.014 0.001 TYR Q 76 PHE 0.010 0.001 PHE J 77 TRP 0.003 0.000 TRP X 117 HIS 0.001 0.000 HIS X 95 Details of bonding type rmsd covalent geometry : bond 0.00226 (21804) covalent geometry : angle 0.42142 (29652) hydrogen bonds : bond 0.03012 ( 1632) hydrogen bonds : angle 3.32420 ( 4824) *********************** 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 333 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 257 time to evaluate : 0.604 Fit side-chains REVERT: B 73 TYR cc_start: 0.8774 (m-80) cc_final: 0.8547 (m-80) REVERT: B 100 PRO cc_start: 0.8071 (Cg_endo) cc_final: 0.7723 (Cg_exo) REVERT: C 5 GLU cc_start: 0.8098 (mp0) cc_final: 0.7653 (mm-30) REVERT: C 17 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7883 (mtmt) REVERT: C 33 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7171 (mmmm) REVERT: D 51 GLU cc_start: 0.8634 (tt0) cc_final: 0.8253 (tt0) REVERT: E 5 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7638 (mm-30) REVERT: G 5 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: I 5 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7698 (mm-30) REVERT: J 100 PRO cc_start: 0.8130 (Cg_endo) cc_final: 0.7770 (Cg_exo) REVERT: K 5 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7605 (mm-30) REVERT: N 100 PRO cc_start: 0.8053 (Cg_endo) cc_final: 0.7777 (Cg_exo) REVERT: O 5 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7569 (mm-30) REVERT: Q 5 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7657 (mm-30) REVERT: S 5 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7808 (mm-30) REVERT: U 33 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7598 (tptp) REVERT: V 100 PRO cc_start: 0.8097 (Cg_endo) cc_final: 0.7838 (Cg_exo) REVERT: W 5 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: W 106 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7918 (ptpp) REVERT: X 119 ARG cc_start: 0.6944 (mtm110) cc_final: 0.6653 (mtm110) outliers start: 76 outliers final: 43 residues processed: 298 average time/residue: 0.7468 time to fit residues: 245.4978 Evaluate side-chains 286 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 231 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 D residue 32 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 5 GLU 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 K residue 5 GLU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 5 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 5 GLU Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 33 LYS Chi-restraints excluded: chain U residue 89 ASP 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 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 94 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 228 optimal weight: 0.4980 chunk 173 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.134461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115771 restraints weight = 25739.148| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.62 r_work: 0.3259 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2491 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= 0.098 Angle : 0.432 7.626 29652 Z= 0.220 Chirality : 0.035 0.135 3468 Planarity : 0.004 0.067 3756 Dihedral : 3.357 15.189 2988 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 3.43 % Allowed : 28.30 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.32 (0.16), residues: 2676 helix: 3.09 (0.11), residues: 1824 sheet: 0.27 (0.29), residues: 348 loop : 0.17 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 115 TYR 0.014 0.001 TYR E 76 PHE 0.011 0.001 PHE J 77 TRP 0.003 0.000 TRP V 90 HIS 0.001 0.000 HIS V 95 Details of bonding type rmsd covalent geometry : bond 0.00230 (21804) covalent geometry : angle 0.43216 (29652) hydrogen bonds : bond 0.02957 ( 1632) hydrogen bonds : angle 3.25542 ( 4824) *********************** 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 319 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 244 time to evaluate : 0.678 Fit side-chains REVERT: A 5 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7565 (mm-30) REVERT: B 73 TYR cc_start: 0.8755 (m-80) cc_final: 0.8513 (m-80) REVERT: B 100 PRO cc_start: 0.8071 (Cg_endo) cc_final: 0.7733 (Cg_exo) REVERT: C 5 GLU cc_start: 0.8118 (mp0) cc_final: 0.7702 (mm-30) REVERT: C 17 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7937 (mtmt) REVERT: C 33 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7210 (mmmm) REVERT: E 5 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7715 (mm-30) REVERT: G 5 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7590 (mm-30) REVERT: I 5 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: J 100 PRO cc_start: 0.8161 (Cg_endo) cc_final: 0.7838 (Cg_exo) REVERT: K 5 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7611 (mm-30) REVERT: N 100 PRO cc_start: 0.8069 (Cg_endo) cc_final: 0.7791 (Cg_exo) REVERT: O 5 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: Q 5 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7699 (mm-30) REVERT: Q 32 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7806 (mm) REVERT: R 100 PRO cc_start: 0.8015 (Cg_endo) cc_final: 0.7712 (Cg_exo) REVERT: S 5 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7832 (mm-30) REVERT: T 100 PRO cc_start: 0.8201 (Cg_endo) cc_final: 0.7899 (Cg_exo) REVERT: V 100 PRO cc_start: 0.8062 (Cg_endo) cc_final: 0.7731 (Cg_exo) REVERT: W 5 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7685 (mm-30) REVERT: W 106 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7886 (ptpp) REVERT: X 119 ARG cc_start: 0.6921 (mtm110) cc_final: 0.6714 (mtm110) outliers start: 75 outliers final: 42 residues processed: 284 average time/residue: 0.6718 time to fit residues: 212.1820 Evaluate side-chains 286 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 231 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU 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 33 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 5 GLU 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 K residue 5 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 N residue 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain O residue 5 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 5 GLU Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain 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 89 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 194 optimal weight: 0.9990 chunk 185 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 195 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 chunk 247 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.131965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113080 restraints weight = 25918.033| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.64 r_work: 0.3208 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 21804 Z= 0.131 Angle : 0.466 7.883 29652 Z= 0.234 Chirality : 0.037 0.135 3468 Planarity : 0.004 0.050 3756 Dihedral : 3.443 14.969 2988 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.30 % Allowed : 29.08 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.28 (0.16), residues: 2676 helix: 3.06 (0.11), residues: 1824 sheet: 0.12 (0.29), residues: 348 loop : 0.25 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 115 TYR 0.016 0.001 TYR P 73 PHE 0.011 0.001 PHE J 77 TRP 0.002 0.000 TRP V 90 HIS 0.001 0.001 HIS X 95 Details of bonding type rmsd covalent geometry : bond 0.00318 (21804) covalent geometry : angle 0.46635 (29652) hydrogen bonds : bond 0.03244 ( 1632) hydrogen bonds : angle 3.32155 ( 4824) *********************** 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 316 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 244 time to evaluate : 0.829 Fit side-chains REVERT: A 5 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: B 73 TYR cc_start: 0.8798 (m-80) cc_final: 0.8569 (m-80) REVERT: B 100 PRO cc_start: 0.8082 (Cg_endo) cc_final: 0.7757 (Cg_exo) REVERT: C 5 GLU cc_start: 0.8113 (mp0) cc_final: 0.7695 (mm-30) REVERT: C 17 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8028 (mtmt) REVERT: E 5 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7659 (mm-30) REVERT: G 5 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: G 33 LYS cc_start: 0.7861 (mmmm) cc_final: 0.7563 (tptp) REVERT: I 5 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7635 (mm-30) REVERT: J 100 PRO cc_start: 0.8225 (Cg_endo) cc_final: 0.7891 (Cg_exo) REVERT: K 5 GLU cc_start: 0.8108 (mp0) cc_final: 0.7588 (mm-30) REVERT: M 32 LEU cc_start: 0.8382 (mm) cc_final: 0.8168 (mp) REVERT: N 100 PRO cc_start: 0.8071 (Cg_endo) cc_final: 0.7804 (Cg_exo) REVERT: O 5 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: P 51 GLU cc_start: 0.8862 (tt0) cc_final: 0.8639 (tt0) REVERT: Q 5 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: R 100 PRO cc_start: 0.8102 (Cg_endo) cc_final: 0.7784 (Cg_exo) REVERT: S 5 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7806 (mm-30) REVERT: T 100 PRO cc_start: 0.8236 (Cg_endo) cc_final: 0.7920 (Cg_exo) REVERT: V 100 PRO cc_start: 0.8131 (Cg_endo) cc_final: 0.7795 (Cg_exo) REVERT: W 5 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7663 (mm-30) REVERT: W 106 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7993 (ptpp) REVERT: X 119 ARG cc_start: 0.6964 (mtm110) cc_final: 0.6678 (mtm110) outliers start: 72 outliers final: 44 residues processed: 283 average time/residue: 0.6888 time to fit residues: 216.9781 Evaluate side-chains 288 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 234 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU 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 32 THR 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 E residue 5 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 32 LEU 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 5 GLU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 89 ASP 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 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain O residue 5 GLU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 5 GLU Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR 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 89 ASP Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 106 LYS Chi-restraints excluded: chain X residue 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 234 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.132800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114242 restraints weight = 25920.657| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.60 r_work: 0.3229 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2461 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= 0.126 Angle : 0.469 8.194 29652 Z= 0.235 Chirality : 0.036 0.135 3468 Planarity : 0.004 0.048 3756 Dihedral : 3.458 15.062 2988 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.11 % Allowed : 29.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.30 (0.16), residues: 2676 helix: 3.07 (0.11), residues: 1824 sheet: 0.13 (0.29), residues: 348 loop : 0.29 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 115 TYR 0.016 0.001 TYR P 73 PHE 0.012 0.001 PHE J 77 TRP 0.003 0.000 TRP V 90 HIS 0.001 0.001 HIS X 95 Details of bonding type rmsd covalent geometry : bond 0.00308 (21804) covalent geometry : angle 0.46939 (29652) hydrogen bonds : bond 0.03198 ( 1632) hydrogen bonds : angle 3.31536 ( 4824) *********************** 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 306 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 238 time to evaluate : 0.725 Fit side-chains REVERT: A 5 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7593 (mm-30) REVERT: A 33 LYS cc_start: 0.7617 (mptt) cc_final: 0.7364 (tptp) REVERT: B 73 TYR cc_start: 0.8791 (m-80) cc_final: 0.8569 (m-80) REVERT: B 100 PRO cc_start: 0.8094 (Cg_endo) cc_final: 0.7758 (Cg_exo) REVERT: C 5 GLU cc_start: 0.8111 (mp0) cc_final: 0.7672 (mm-30) REVERT: C 17 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8057 (mtmt) REVERT: E 5 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: G 5 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7587 (mm-30) REVERT: I 5 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: J 100 PRO cc_start: 0.8275 (Cg_endo) cc_final: 0.7909 (Cg_exo) REVERT: K 5 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7639 (mm-30) REVERT: N 100 PRO cc_start: 0.8104 (Cg_endo) cc_final: 0.7837 (Cg_exo) REVERT: O 5 GLU cc_start: 0.8080 (mp0) cc_final: 0.7613 (mm-30) REVERT: Q 5 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: Q 33 LYS cc_start: 0.7703 (mptt) cc_final: 0.7489 (mmmm) REVERT: R 100 PRO cc_start: 0.8101 (Cg_endo) cc_final: 0.7793 (Cg_exo) REVERT: S 5 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7834 (mm-30) REVERT: U 33 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7554 (tptp) REVERT: V 100 PRO cc_start: 0.8174 (Cg_endo) cc_final: 0.7818 (Cg_exo) REVERT: W 5 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: W 106 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8030 (ptpp) REVERT: X 119 ARG cc_start: 0.7041 (mtm110) cc_final: 0.6751 (mtm110) outliers start: 68 outliers final: 45 residues processed: 278 average time/residue: 0.6950 time to fit residues: 215.5603 Evaluate side-chains 288 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 232 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU 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 32 THR 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 E residue 5 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 5 GLU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 5 GLU Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR 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 33 LYS 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 5 GLU Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 106 LYS Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 54 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 208 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 100 optimal weight: 0.0000 chunk 102 optimal weight: 0.8980 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.134971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116263 restraints weight = 25694.224| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.63 r_work: 0.3250 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2603 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= 0.095 Angle : 0.454 8.607 29652 Z= 0.227 Chirality : 0.035 0.134 3468 Planarity : 0.004 0.048 3756 Dihedral : 3.383 15.289 2988 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.75 % Allowed : 29.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.43 (0.16), residues: 2676 helix: 3.16 (0.11), residues: 1824 sheet: 0.25 (0.29), residues: 348 loop : 0.33 (0.31), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 115 TYR 0.014 0.001 TYR P 73 PHE 0.010 0.001 PHE J 77 TRP 0.004 0.001 TRP X 117 HIS 0.001 0.000 HIS V 95 Details of bonding type rmsd covalent geometry : bond 0.00219 (21804) covalent geometry : angle 0.45375 (29652) hydrogen bonds : bond 0.02906 ( 1632) hydrogen bonds : angle 3.24369 ( 4824) ********************** 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 297 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 237 time to evaluate : 0.757 Fit side-chains REVERT: B 73 TYR cc_start: 0.8761 (m-80) cc_final: 0.8526 (m-80) REVERT: B 100 PRO cc_start: 0.8051 (Cg_endo) cc_final: 0.7709 (Cg_exo) REVERT: C 5 GLU cc_start: 0.8071 (mp0) cc_final: 0.7594 (mm-30) REVERT: C 17 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7896 (mtmt) REVERT: E 5 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: G 5 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7539 (mm-30) REVERT: G 33 LYS cc_start: 0.7843 (mmmm) cc_final: 0.7527 (tptp) REVERT: I 5 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7585 (mm-30) REVERT: J 100 PRO cc_start: 0.8242 (Cg_endo) cc_final: 0.7875 (Cg_exo) REVERT: K 5 GLU cc_start: 0.8110 (mp0) cc_final: 0.7595 (mm-30) REVERT: N 100 PRO cc_start: 0.8052 (Cg_endo) cc_final: 0.7795 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7990 (mp0) cc_final: 0.7480 (mm-30) REVERT: R 100 PRO cc_start: 0.7985 (Cg_endo) cc_final: 0.7700 (Cg_exo) REVERT: S 5 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7734 (mm-30) REVERT: T 100 PRO cc_start: 0.8114 (Cg_endo) cc_final: 0.7787 (Cg_exo) REVERT: V 100 PRO cc_start: 0.8099 (Cg_endo) cc_final: 0.7708 (Cg_exo) REVERT: W 5 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7628 (mm-30) REVERT: W 106 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7880 (ptpp) REVERT: X 119 ARG cc_start: 0.6908 (mtm110) cc_final: 0.6604 (mtm110) outliers start: 60 outliers final: 42 residues processed: 272 average time/residue: 0.6773 time to fit residues: 205.3753 Evaluate side-chains 279 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 32 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 5 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 L residue 45 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain S residue 5 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 89 ASP Chi-restraints excluded: chain V residue 45 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 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 181 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 161 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.133190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114294 restraints weight = 25903.677| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.65 r_work: 0.3225 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21804 Z= 0.117 Angle : 0.467 8.451 29652 Z= 0.233 Chirality : 0.036 0.134 3468 Planarity : 0.004 0.049 3756 Dihedral : 3.411 15.157 2988 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.75 % Allowed : 29.90 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.41 (0.16), residues: 2676 helix: 3.14 (0.11), residues: 1824 sheet: 0.20 (0.29), residues: 348 loop : 0.37 (0.31), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 115 TYR 0.016 0.001 TYR P 73 PHE 0.011 0.001 PHE R 77 TRP 0.003 0.000 TRP X 117 HIS 0.001 0.001 HIS T 95 Details of bonding type rmsd covalent geometry : bond 0.00283 (21804) covalent geometry : angle 0.46734 (29652) hydrogen bonds : bond 0.03113 ( 1632) hydrogen bonds : angle 3.28699 ( 4824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6160.13 seconds wall clock time: 105 minutes 37.97 seconds (6337.97 seconds total)