Starting phenix.real_space_refine on Wed May 21 01:00:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ump_42381/05_2025/8ump_42381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ump_42381/05_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_42381/05_2025/8ump_42381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ump_42381/05_2025/8ump_42381.map" model { file = "/net/cci-nas-00/data/ceres_data/8ump_42381/05_2025/8ump_42381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ump_42381/05_2025/8ump_42381.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 13764 2.51 5 N 3564 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21432 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "B" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, W, D, F, H, J, L, N, P, R, T, V, X Time building chain proxies: 6.15, per 1000 atoms: 0.29 Number of scatterers: 21432 At special positions: 0 Unit cell: (138.938, 131.625, 126.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 4080 8.00 N 3564 7.00 C 13764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.61 Conformation dependent library (CDL) restraints added in 2.9 seconds 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5232 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 24 sheets defined 66.1% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 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: 5.84 Time building geometry restraints manager: 6.47 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: 0.19 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: 1.130 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: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 40.070 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.080 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:9.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.890 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.15), residues: 2676 helix: 1.38 (0.11), residues: 1764 sheet: -0.63 (0.25), residues: 348 loop : 0.14 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 90 HIS 0.002 0.001 HIS F 95 PHE 0.008 0.001 PHE D 77 TYR 0.016 0.002 TYR X 73 ARG 0.011 0.001 ARG P 115 Details of bonding type rmsd hydrogen bonds : bond 0.19611 ( 1632) hydrogen bonds : angle 6.11215 ( 4824) covalent geometry : bond 0.00670 (21804) covalent geometry : angle 0.73597 (29652) *********************** 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 : 2.196 Fit side-chains REVERT: G 5 GLU cc_start: 0.7655 (mp0) cc_final: 0.7157 (mm-30) REVERT: K 5 GLU cc_start: 0.7585 (mp0) cc_final: 0.7253 (mm-30) REVERT: N 115 ARG cc_start: 0.7073 (ttt-90) cc_final: 0.6760 (ttt-90) REVERT: O 5 GLU cc_start: 0.7624 (mp0) cc_final: 0.7250 (mm-30) REVERT: P 81 ARG cc_start: 0.7986 (ptp90) cc_final: 0.7771 (ptt-90) REVERT: V 83 ARG cc_start: 0.8663 (mtp180) cc_final: 0.8373 (mmt180) outliers start: 15 outliers final: 2 residues processed: 261 average time/residue: 1.4039 time to fit residues: 413.0043 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 : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain U residue 89 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 106 optimal weight: 0.2980 chunk 206 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 239 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN C 19 ASN C 37 ASN E 37 ASN G 37 ASN I 37 ASN K 37 ASN M 37 ASN O 37 ASN Q 37 ASN S 37 ASN U 37 ASN W 37 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.134035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115108 restraints weight = 25554.470| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.65 r_work: 0.3257 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21804 Z= 0.115 Angle : 0.472 5.212 29652 Z= 0.246 Chirality : 0.036 0.129 3468 Planarity : 0.003 0.040 3756 Dihedral : 3.735 24.358 2992 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 3.89 % Allowed : 23.86 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.16), residues: 2676 helix: 2.22 (0.11), residues: 1824 sheet: 0.14 (0.27), residues: 324 loop : 0.12 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 75 HIS 0.000 0.000 HIS J 95 PHE 0.012 0.002 PHE J 77 TYR 0.016 0.001 TYR O 76 ARG 0.006 0.001 ARG N 115 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 1632) hydrogen bonds : angle 3.80503 ( 4824) covalent geometry : bond 0.00292 (21804) covalent geometry : angle 0.47217 (29652) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 303 time to evaluate : 2.313 Fit side-chains REVERT: B 73 TYR cc_start: 0.8829 (m-80) cc_final: 0.8600 (m-80) REVERT: B 94 ARG cc_start: 0.8581 (mmm160) cc_final: 0.8340 (mmm-85) REVERT: B 100 PRO cc_start: 0.8103 (Cg_endo) cc_final: 0.7769 (Cg_exo) REVERT: D 94 ARG cc_start: 0.8579 (mmm160) cc_final: 0.8221 (mmm-85) REVERT: F 100 PRO cc_start: 0.8128 (Cg_endo) cc_final: 0.7775 (Cg_exo) REVERT: G 5 GLU cc_start: 0.8024 (mp0) cc_final: 0.7463 (mm-30) REVERT: H 100 PRO cc_start: 0.7951 (Cg_endo) cc_final: 0.7615 (Cg_exo) REVERT: J 74 ARG cc_start: 0.8308 (ttm170) cc_final: 0.8069 (ttm170) REVERT: J 94 ARG cc_start: 0.8651 (mmm160) cc_final: 0.8390 (mmm-85) REVERT: K 5 GLU cc_start: 0.7995 (mp0) cc_final: 0.7474 (mm-30) REVERT: N 94 ARG cc_start: 0.8517 (mmm160) cc_final: 0.8270 (mmm-85) REVERT: N 115 ARG cc_start: 0.7317 (ttt-90) cc_final: 0.6902 (ttt-90) REVERT: O 5 GLU cc_start: 0.7884 (mp0) cc_final: 0.7444 (mm-30) REVERT: P 83 ARG cc_start: 0.8427 (mmm160) cc_final: 0.8197 (mtp180) REVERT: P 94 ARG cc_start: 0.8637 (mmm160) cc_final: 0.8401 (mmm-85) REVERT: P 100 PRO cc_start: 0.8008 (Cg_endo) cc_final: 0.7702 (Cg_exo) REVERT: R 94 ARG cc_start: 0.8663 (mmm160) cc_final: 0.8451 (mmm-85) REVERT: S 5 GLU cc_start: 0.8039 (mp0) cc_final: 0.7461 (mm-30) REVERT: T 94 ARG cc_start: 0.8620 (mmm160) cc_final: 0.8370 (mmm-85) REVERT: V 92 GLN cc_start: 0.8312 (mt0) cc_final: 0.8107 (mm110) REVERT: W 5 GLU cc_start: 0.8037 (mp0) cc_final: 0.7488 (mm-30) REVERT: W 32 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7590 (mp) REVERT: X 100 PRO cc_start: 0.7988 (Cg_endo) cc_final: 0.7668 (Cg_exo) outliers start: 85 outliers final: 24 residues processed: 336 average time/residue: 2.1155 time to fit residues: 770.4385 Evaluate side-chains 238 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 32 LEU Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain X residue 45 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 178 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN D 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112438 restraints weight = 25537.881| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.64 r_work: 0.3219 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21804 Z= 0.141 Angle : 0.464 5.229 29652 Z= 0.239 Chirality : 0.036 0.134 3468 Planarity : 0.004 0.045 3756 Dihedral : 3.541 14.909 2988 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.26 % Allowed : 25.00 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.16), residues: 2676 helix: 2.55 (0.11), residues: 1824 sheet: -0.03 (0.28), residues: 348 loop : 0.27 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 117 HIS 0.002 0.001 HIS H 95 PHE 0.012 0.001 PHE J 77 TYR 0.013 0.001 TYR I 76 ARG 0.007 0.001 ARG R 61 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 1632) hydrogen bonds : angle 3.60928 ( 4824) covalent geometry : bond 0.00343 (21804) covalent geometry : angle 0.46357 (29652) *********************** 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 370 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 277 time to evaluate : 2.337 Fit side-chains REVERT: B 100 PRO cc_start: 0.8107 (Cg_endo) cc_final: 0.7838 (Cg_exo) REVERT: E 5 GLU cc_start: 0.8073 (mp0) cc_final: 0.7577 (mm-30) REVERT: F 100 PRO cc_start: 0.8145 (Cg_endo) cc_final: 0.7871 (Cg_exo) REVERT: G 5 GLU cc_start: 0.8100 (mp0) cc_final: 0.7566 (mm-30) REVERT: H 100 PRO cc_start: 0.7961 (Cg_endo) cc_final: 0.7706 (Cg_exo) REVERT: I 5 GLU cc_start: 0.8043 (mp0) cc_final: 0.7494 (mm-30) REVERT: J 100 PRO cc_start: 0.8133 (Cg_endo) cc_final: 0.7788 (Cg_exo) REVERT: K 5 GLU cc_start: 0.8088 (mp0) cc_final: 0.7611 (mm-30) REVERT: M 33 LYS cc_start: 0.7581 (mptt) cc_final: 0.6966 (mmmm) REVERT: O 5 GLU cc_start: 0.8096 (mp0) cc_final: 0.7674 (mm-30) REVERT: P 74 ARG cc_start: 0.8404 (ttm170) cc_final: 0.8153 (ttm170) REVERT: P 94 ARG cc_start: 0.8745 (mmm160) cc_final: 0.8536 (mmm-85) REVERT: P 100 PRO cc_start: 0.7912 (Cg_endo) cc_final: 0.7684 (Cg_exo) REVERT: Q 5 GLU cc_start: 0.8156 (mp0) cc_final: 0.7576 (mm-30) REVERT: S 5 GLU cc_start: 0.8125 (mp0) cc_final: 0.7631 (mm-30) REVERT: T 94 ARG cc_start: 0.8694 (mmm160) cc_final: 0.8440 (mmm-85) REVERT: V 92 GLN cc_start: 0.8280 (mt0) cc_final: 0.8021 (mm110) REVERT: W 5 GLU cc_start: 0.8101 (mp0) cc_final: 0.7598 (mm-30) REVERT: W 106 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8106 (ptpp) REVERT: X 100 PRO cc_start: 0.7981 (Cg_endo) cc_final: 0.7740 (Cg_exo) outliers start: 93 outliers final: 35 residues processed: 325 average time/residue: 1.8211 time to fit residues: 649.6633 Evaluate side-chains 255 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 2.186 ------------------------------------------------------------------------------- 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 106 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 107 THR 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 O residue 89 ASP Chi-restraints excluded: chain Q residue 32 LEU 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 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 89 ASP Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 106 LYS Chi-restraints excluded: chain X residue 55 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 115 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 126 optimal weight: 0.0980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.133124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114033 restraints weight = 25914.312| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.66 r_work: 0.3228 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21804 Z= 0.113 Angle : 0.437 6.536 29652 Z= 0.225 Chirality : 0.035 0.136 3468 Planarity : 0.004 0.043 3756 Dihedral : 3.470 15.167 2988 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.75 % Allowed : 25.78 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.16), residues: 2676 helix: 2.73 (0.11), residues: 1824 sheet: 0.12 (0.29), residues: 348 loop : 0.13 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 117 HIS 0.001 0.001 HIS H 95 PHE 0.011 0.001 PHE J 77 TYR 0.014 0.001 TYR Q 76 ARG 0.008 0.001 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 1632) hydrogen bonds : angle 3.46112 ( 4824) covalent geometry : bond 0.00274 (21804) covalent geometry : angle 0.43668 (29652) *********************** 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: 82 poor density : 276 time to evaluate : 2.227 Fit side-chains REVERT: B 94 ARG cc_start: 0.8736 (mmm160) cc_final: 0.8473 (mmm-85) REVERT: B 100 PRO cc_start: 0.8073 (Cg_endo) cc_final: 0.7843 (Cg_exo) REVERT: C 17 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7927 (mtmt) REVERT: F 100 PRO cc_start: 0.8124 (Cg_endo) cc_final: 0.7921 (Cg_exo) REVERT: G 5 GLU cc_start: 0.8037 (mp0) cc_final: 0.7497 (mm-30) REVERT: G 33 LYS cc_start: 0.7399 (mptt) cc_final: 0.6956 (mmmt) REVERT: H 100 PRO cc_start: 0.7711 (Cg_endo) cc_final: 0.7505 (Cg_exo) REVERT: I 5 GLU cc_start: 0.8103 (mp0) cc_final: 0.7587 (mm-30) REVERT: I 33 LYS cc_start: 0.7669 (mmmm) cc_final: 0.7338 (tptp) REVERT: J 100 PRO cc_start: 0.8112 (Cg_endo) cc_final: 0.7773 (Cg_exo) REVERT: K 5 GLU cc_start: 0.8040 (mp0) cc_final: 0.7540 (mm-30) REVERT: L 46 LYS cc_start: 0.8818 (ptpp) cc_final: 0.8563 (ptmt) REVERT: N 100 PRO cc_start: 0.7999 (Cg_endo) cc_final: 0.7709 (Cg_exo) REVERT: O 5 GLU cc_start: 0.8004 (mp0) cc_final: 0.7550 (mm-30) REVERT: Q 5 GLU cc_start: 0.8137 (mp0) cc_final: 0.7508 (mm-30) REVERT: S 5 GLU cc_start: 0.8160 (mp0) cc_final: 0.7663 (mm-30) REVERT: V 100 PRO cc_start: 0.8126 (Cg_endo) cc_final: 0.7750 (Cg_exo) REVERT: W 5 GLU cc_start: 0.8023 (mp0) cc_final: 0.7484 (mm-30) REVERT: W 106 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.8018 (ptpp) outliers start: 82 outliers final: 41 residues processed: 316 average time/residue: 1.8205 time to fit residues: 630.6003 Evaluate side-chains 278 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain 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 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 121 SER Chi-restraints excluded: chain W residue 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 121 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 118 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 172 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 173 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 256 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.134616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115714 restraints weight = 25752.835| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.64 r_work: 0.3258 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21804 Z= 0.098 Angle : 0.427 7.095 29652 Z= 0.220 Chirality : 0.035 0.134 3468 Planarity : 0.004 0.062 3756 Dihedral : 3.401 15.379 2988 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.48 % Allowed : 27.11 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.16), residues: 2676 helix: 2.91 (0.11), residues: 1824 sheet: 0.23 (0.28), residues: 372 loop : 0.27 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 117 HIS 0.001 0.000 HIS H 95 PHE 0.010 0.001 PHE B 77 TYR 0.013 0.001 TYR M 76 ARG 0.009 0.001 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.03034 ( 1632) hydrogen bonds : angle 3.36736 ( 4824) covalent geometry : bond 0.00232 (21804) covalent geometry : angle 0.42736 (29652) *********************** 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 346 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 270 time to evaluate : 2.287 Fit side-chains REVERT: A 5 GLU cc_start: 0.7946 (mp0) cc_final: 0.7392 (mm-30) REVERT: C 17 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7730 (mtmt) REVERT: G 5 GLU cc_start: 0.7878 (mp0) cc_final: 0.7258 (mm-30) REVERT: G 33 LYS cc_start: 0.7330 (mptt) cc_final: 0.6864 (mmmt) REVERT: I 5 GLU cc_start: 0.7889 (mp0) cc_final: 0.7349 (mm-30) REVERT: I 33 LYS cc_start: 0.7606 (mmmm) cc_final: 0.7347 (tptp) REVERT: J 100 PRO cc_start: 0.8039 (Cg_endo) cc_final: 0.7701 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7898 (mp0) cc_final: 0.7369 (mm-30) REVERT: L 46 LYS cc_start: 0.8732 (ptpp) cc_final: 0.8495 (ptmt) REVERT: N 100 PRO cc_start: 0.7963 (Cg_endo) cc_final: 0.7628 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7808 (mp0) cc_final: 0.7306 (mm-30) REVERT: Q 5 GLU cc_start: 0.7971 (mp0) cc_final: 0.7355 (mm-30) REVERT: S 5 GLU cc_start: 0.7976 (mp0) cc_final: 0.7425 (mm-30) REVERT: V 92 GLN cc_start: 0.8130 (mt0) cc_final: 0.7861 (mm110) REVERT: V 100 PRO cc_start: 0.8001 (Cg_endo) cc_final: 0.7729 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7893 (mp0) cc_final: 0.7327 (mm-30) REVERT: W 106 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7790 (ptpp) outliers start: 76 outliers final: 40 residues processed: 309 average time/residue: 1.7086 time to fit residues: 584.1235 Evaluate side-chains 281 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain 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 67 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 247 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 174 optimal weight: 0.0970 chunk 212 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.135111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116316 restraints weight = 25603.952| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.63 r_work: 0.3274 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2350 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= 0.094 Angle : 0.424 7.353 29652 Z= 0.217 Chirality : 0.035 0.133 3468 Planarity : 0.004 0.069 3756 Dihedral : 3.361 15.481 2988 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.02 % Allowed : 28.53 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.16), residues: 2676 helix: 3.04 (0.11), residues: 1824 sheet: 0.38 (0.28), residues: 372 loop : 0.30 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP X 117 HIS 0.001 0.000 HIS P 95 PHE 0.011 0.001 PHE B 77 TYR 0.013 0.001 TYR Q 76 ARG 0.008 0.001 ARG F 115 Details of bonding type rmsd hydrogen bonds : bond 0.02941 ( 1632) hydrogen bonds : angle 3.29078 ( 4824) covalent geometry : bond 0.00219 (21804) covalent geometry : angle 0.42384 (29652) *********************** 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 329 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 263 time to evaluate : 2.181 Fit side-chains REVERT: A 5 GLU cc_start: 0.8154 (mp0) cc_final: 0.7663 (mm-30) REVERT: A 33 LYS cc_start: 0.7160 (mptt) cc_final: 0.6785 (tptp) REVERT: C 17 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7963 (mtmt) REVERT: D 51 GLU cc_start: 0.8561 (tt0) cc_final: 0.8134 (tt0) REVERT: E 5 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7658 (mm-30) REVERT: F 115 ARG cc_start: 0.7307 (ttt-90) cc_final: 0.6989 (ttt90) REVERT: G 5 GLU cc_start: 0.8079 (mp0) cc_final: 0.7542 (mm-30) REVERT: G 33 LYS cc_start: 0.7409 (mptt) cc_final: 0.6991 (mmmm) REVERT: I 5 GLU cc_start: 0.8019 (mp0) cc_final: 0.7608 (mm-30) REVERT: I 33 LYS cc_start: 0.7920 (mmmm) cc_final: 0.7708 (tptp) REVERT: J 100 PRO cc_start: 0.8160 (Cg_endo) cc_final: 0.7851 (Cg_exo) REVERT: K 5 GLU cc_start: 0.8102 (mp0) cc_final: 0.7638 (mm-30) REVERT: N 100 PRO cc_start: 0.8063 (Cg_endo) cc_final: 0.7746 (Cg_exo) REVERT: O 5 GLU cc_start: 0.8058 (mp0) cc_final: 0.7595 (mm-30) REVERT: Q 5 GLU cc_start: 0.8215 (mp0) cc_final: 0.7644 (mm-30) REVERT: R 100 PRO cc_start: 0.8005 (Cg_endo) cc_final: 0.7677 (Cg_exo) REVERT: S 5 GLU cc_start: 0.8219 (mp0) cc_final: 0.7752 (mm-30) REVERT: T 100 PRO cc_start: 0.8121 (Cg_endo) cc_final: 0.7793 (Cg_exo) REVERT: U 32 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8041 (mp) REVERT: V 92 GLN cc_start: 0.8267 (mt0) cc_final: 0.8024 (mm110) REVERT: V 100 PRO cc_start: 0.8030 (Cg_endo) cc_final: 0.7771 (Cg_exo) REVERT: W 5 GLU cc_start: 0.8112 (mp0) cc_final: 0.7610 (mm-30) REVERT: W 106 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7895 (ptpp) outliers start: 66 outliers final: 43 residues processed: 294 average time/residue: 1.6316 time to fit residues: 530.7357 Evaluate side-chains 285 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 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 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 H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 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 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain 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 121 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 181 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 243 optimal weight: 5.9990 chunk 252 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.132597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113770 restraints weight = 25702.807| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.63 r_work: 0.3231 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2305 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= 0.129 Angle : 0.459 7.600 29652 Z= 0.231 Chirality : 0.036 0.137 3468 Planarity : 0.004 0.053 3756 Dihedral : 3.423 15.289 2988 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.62 % Allowed : 28.25 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.16), residues: 2676 helix: 3.05 (0.11), residues: 1824 sheet: 0.26 (0.29), residues: 348 loop : 0.23 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 41 HIS 0.001 0.001 HIS H 95 PHE 0.012 0.001 PHE J 77 TYR 0.015 0.001 TYR P 73 ARG 0.008 0.001 ARG F 115 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 1632) hydrogen bonds : angle 3.32502 ( 4824) covalent geometry : bond 0.00315 (21804) covalent geometry : angle 0.45906 (29652) *********************** 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 325 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 246 time to evaluate : 2.343 Fit side-chains REVERT: A 33 LYS cc_start: 0.7347 (mptt) cc_final: 0.6839 (tptp) REVERT: C 5 GLU cc_start: 0.7911 (mp0) cc_final: 0.7347 (mm-30) REVERT: C 33 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6891 (mmmm) REVERT: D 51 GLU cc_start: 0.8684 (tt0) cc_final: 0.8260 (tt0) REVERT: E 5 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7379 (mm-30) REVERT: F 115 ARG cc_start: 0.6980 (ttt-90) cc_final: 0.6685 (ttt90) REVERT: G 5 GLU cc_start: 0.7884 (mp0) cc_final: 0.7303 (mm-30) REVERT: G 33 LYS cc_start: 0.7369 (mptt) cc_final: 0.6939 (mmmm) REVERT: I 5 GLU cc_start: 0.7745 (mp0) cc_final: 0.7296 (mm-30) REVERT: J 51 GLU cc_start: 0.8963 (tt0) cc_final: 0.8724 (tt0) REVERT: J 62 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7704 (ttt-90) REVERT: J 100 PRO cc_start: 0.8166 (Cg_endo) cc_final: 0.7791 (Cg_exo) REVERT: K 5 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7326 (mm-30) REVERT: N 100 PRO cc_start: 0.8010 (Cg_endo) cc_final: 0.7675 (Cg_exo) REVERT: O 5 GLU cc_start: 0.7856 (mp0) cc_final: 0.7316 (mm-30) REVERT: Q 5 GLU cc_start: 0.7965 (mp0) cc_final: 0.7353 (mm-30) REVERT: R 62 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7506 (ttt-90) REVERT: R 100 PRO cc_start: 0.7849 (Cg_endo) cc_final: 0.7530 (Cg_exo) REVERT: S 5 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: T 100 PRO cc_start: 0.8044 (Cg_endo) cc_final: 0.7710 (Cg_exo) REVERT: U 32 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7996 (mp) REVERT: V 92 GLN cc_start: 0.8157 (mt0) cc_final: 0.7854 (mm110) REVERT: V 100 PRO cc_start: 0.7959 (Cg_endo) cc_final: 0.7691 (Cg_exo) REVERT: W 5 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7354 (mm-30) REVERT: W 106 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7842 (ptpp) outliers start: 79 outliers final: 47 residues processed: 290 average time/residue: 1.5246 time to fit residues: 493.1452 Evaluate side-chains 293 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 237 time to evaluate : 2.315 ------------------------------------------------------------------------------- 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 33 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 70 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 62 ARG 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 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 O residue 46 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 62 ARG Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 32 LEU Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 121 SER Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 106 LYS Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 31 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 198 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108463 restraints weight = 26343.925| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.65 r_work: 0.3148 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 21804 Z= 0.258 Angle : 0.567 7.630 29652 Z= 0.281 Chirality : 0.041 0.138 3468 Planarity : 0.004 0.048 3756 Dihedral : 3.739 15.089 2988 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.94 % Allowed : 27.93 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.16), residues: 2676 helix: 2.75 (0.11), residues: 1824 sheet: -0.11 (0.28), residues: 348 loop : 0.26 (0.30), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 41 HIS 0.004 0.002 HIS X 95 PHE 0.014 0.002 PHE J 77 TYR 0.021 0.002 TYR P 73 ARG 0.009 0.001 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 1632) hydrogen bonds : angle 3.58268 ( 4824) covalent geometry : bond 0.00647 (21804) covalent geometry : angle 0.56702 (29652) *********************** 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 334 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 248 time to evaluate : 2.239 Fit side-chains REVERT: A 33 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7455 (tptp) REVERT: C 17 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8158 (mtmt) REVERT: C 33 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7300 (mmmm) REVERT: D 119 ARG cc_start: 0.6893 (mtm110) cc_final: 0.6664 (mtm110) REVERT: E 5 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7643 (mm-30) REVERT: F 115 ARG cc_start: 0.7301 (ttt-90) cc_final: 0.6990 (ttt90) REVERT: G 5 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7514 (mm-30) REVERT: G 33 LYS cc_start: 0.7678 (mptt) cc_final: 0.7459 (mmmm) REVERT: I 5 GLU cc_start: 0.8023 (mp0) cc_final: 0.7613 (mm-30) REVERT: K 5 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: N 100 PRO cc_start: 0.8265 (Cg_endo) cc_final: 0.7908 (Cg_exo) REVERT: O 5 GLU cc_start: 0.8090 (mp0) cc_final: 0.7632 (mm-30) REVERT: Q 5 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7671 (mm-30) REVERT: S 5 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7827 (mm-30) REVERT: V 100 PRO cc_start: 0.8325 (Cg_endo) cc_final: 0.7940 (Cg_exo) REVERT: W 5 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7719 (mm-30) REVERT: W 33 LYS cc_start: 0.8118 (mmmm) cc_final: 0.7875 (tptp) outliers start: 86 outliers final: 45 residues processed: 298 average time/residue: 1.6038 time to fit residues: 531.1595 Evaluate side-chains 285 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 231 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 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 J residue 45 GLU Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 5 GLU Chi-restraints excluded: chain Q residue 89 ASP Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 121 SER Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 121 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 192 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 223 optimal weight: 0.6980 chunk 256 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.132789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113942 restraints weight = 25834.760| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.64 r_work: 0.3222 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2441 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= 0.110 Angle : 0.466 8.290 29652 Z= 0.234 Chirality : 0.036 0.136 3468 Planarity : 0.004 0.048 3756 Dihedral : 3.541 15.089 2988 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.70 % Allowed : 29.44 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.16), residues: 2676 helix: 2.96 (0.11), residues: 1824 sheet: -0.04 (0.27), residues: 372 loop : 0.34 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 117 HIS 0.001 0.001 HIS H 95 PHE 0.011 0.001 PHE B 77 TYR 0.015 0.001 TYR X 73 ARG 0.010 0.001 ARG X 115 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 1632) hydrogen bonds : angle 3.34306 ( 4824) covalent geometry : bond 0.00261 (21804) covalent geometry : angle 0.46552 (29652) *********************** 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 298 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 239 time to evaluate : 2.215 Fit side-chains REVERT: A 33 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7170 (tptp) REVERT: C 5 GLU cc_start: 0.8130 (mp0) cc_final: 0.7725 (mm-30) REVERT: C 17 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7950 (mtmt) REVERT: C 33 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.7169 (mmmm) REVERT: E 5 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7647 (mm-30) REVERT: F 115 ARG cc_start: 0.7244 (ttt-90) cc_final: 0.6925 (ttt90) REVERT: G 33 LYS cc_start: 0.7564 (mptt) cc_final: 0.7217 (mmmm) REVERT: I 5 GLU cc_start: 0.7956 (mp0) cc_final: 0.7535 (mm-30) REVERT: K 5 GLU cc_start: 0.8048 (mp0) cc_final: 0.7567 (mm-30) REVERT: N 100 PRO cc_start: 0.8153 (Cg_endo) cc_final: 0.7770 (Cg_exo) REVERT: O 5 GLU cc_start: 0.8042 (mp0) cc_final: 0.7556 (mm-30) REVERT: Q 5 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7667 (mm-30) REVERT: S 5 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7780 (mm-30) REVERT: V 100 PRO cc_start: 0.8202 (Cg_endo) cc_final: 0.7835 (Cg_exo) REVERT: W 5 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7642 (mm-30) REVERT: X 115 ARG cc_start: 0.7269 (ttt-90) cc_final: 0.7032 (ttt90) outliers start: 59 outliers final: 39 residues processed: 275 average time/residue: 1.5269 time to fit residues: 467.8730 Evaluate side-chains 274 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 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 G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 5 GLU Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 121 SER Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain 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 30 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 255 optimal weight: 0.0020 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 32 optimal weight: 0.0270 overall best weight: 1.8050 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.131462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112478 restraints weight = 26107.067| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.66 r_work: 0.3200 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2408 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= 0.139 Angle : 0.492 8.409 29652 Z= 0.244 Chirality : 0.037 0.136 3468 Planarity : 0.004 0.047 3756 Dihedral : 3.540 15.008 2988 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.56 % Allowed : 29.53 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.16 (0.16), residues: 2676 helix: 2.96 (0.11), residues: 1824 sheet: -0.04 (0.27), residues: 372 loop : 0.39 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP V 117 HIS 0.002 0.001 HIS X 95 PHE 0.012 0.001 PHE J 77 TYR 0.019 0.001 TYR P 73 ARG 0.010 0.001 ARG N 115 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 1632) hydrogen bonds : angle 3.38740 ( 4824) covalent geometry : bond 0.00339 (21804) covalent geometry : angle 0.49180 (29652) ********************** 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 286 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 230 time to evaluate : 2.321 Fit side-chains REVERT: A 33 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7208 (tptp) REVERT: C 5 GLU cc_start: 0.8143 (mp0) cc_final: 0.7681 (mm-30) REVERT: C 17 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8015 (mtmt) REVERT: C 33 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7207 (mmmm) REVERT: E 5 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7628 (mm-30) REVERT: F 115 ARG cc_start: 0.7227 (ttt-90) cc_final: 0.6917 (ttt90) REVERT: G 33 LYS cc_start: 0.7522 (mptt) cc_final: 0.7249 (mmmm) REVERT: I 5 GLU cc_start: 0.7925 (mp0) cc_final: 0.7520 (mm-30) REVERT: K 5 GLU cc_start: 0.8067 (mp0) cc_final: 0.7551 (mm-30) REVERT: N 100 PRO cc_start: 0.8172 (Cg_endo) cc_final: 0.7796 (Cg_exo) REVERT: O 5 GLU cc_start: 0.8052 (mp0) cc_final: 0.7554 (mm-30) REVERT: Q 5 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7686 (mm-30) REVERT: S 5 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7780 (mm-30) REVERT: V 100 PRO cc_start: 0.8116 (Cg_endo) cc_final: 0.7754 (Cg_exo) REVERT: W 5 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7643 (mm-30) outliers start: 56 outliers final: 44 residues processed: 266 average time/residue: 1.4890 time to fit residues: 443.1273 Evaluate side-chains 279 residues out of total 2184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 228 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 45 GLU Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain P residue 55 THR Chi-restraints excluded: chain P residue 121 SER Chi-restraints excluded: chain Q residue 5 GLU Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain S residue 5 GLU Chi-restraints excluded: chain S residue 89 ASP Chi-restraints excluded: chain T residue 45 GLU Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 106 THR Chi-restraints excluded: chain T residue 121 SER Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 121 SER Chi-restraints excluded: chain W residue 5 GLU Chi-restraints excluded: chain W residue 22 THR Chi-restraints excluded: chain W residue 46 GLU Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain 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 69 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 219 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 148 optimal weight: 0.0770 chunk 178 optimal weight: 0.7980 chunk 202 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.133450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114672 restraints weight = 25858.959| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.63 r_work: 0.3246 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2529 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= 0.111 Angle : 0.467 8.521 29652 Z= 0.232 Chirality : 0.036 0.136 3468 Planarity : 0.004 0.047 3756 Dihedral : 3.461 15.108 2988 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.61 % Allowed : 29.40 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.16), residues: 2676 helix: 3.05 (0.11), residues: 1824 sheet: 0.09 (0.28), residues: 372 loop : 0.39 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 117 HIS 0.001 0.001 HIS T 95 PHE 0.011 0.001 PHE R 77 TYR 0.015 0.001 TYR H 73 ARG 0.009 0.001 ARG N 115 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 1632) hydrogen bonds : angle 3.31345 ( 4824) covalent geometry : bond 0.00264 (21804) covalent geometry : angle 0.46747 (29652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14409.54 seconds wall clock time: 248 minutes 33.18 seconds (14913.18 seconds total)