Starting phenix.real_space_refine on Sat Oct 24 03:32:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10gm_75155/10_2026/10gm_75155.cif Found real_map, /net/cci-nas-00/data/ceres_data/10gm_75155/10_2026/10gm_75155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10gm_75155/10_2026/10gm_75155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10gm_75155/10_2026/10gm_75155.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10gm_75155/10_2026/10gm_75155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10gm_75155/10_2026/10gm_75155.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 10 5.16 5 C 6657 2.51 5 N 2263 2.21 5 O 2825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12049 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2997 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 147, 2997 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3033 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 2.45, per 1000 atoms: 0.20 Number of scatterers: 12049 At special positions: 0 Unit cell: (73.8375, 122.925, 117.562, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 294 15.00 O 2825 8.00 N 2263 7.00 C 6657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 451.0 milliseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1418 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 72.9% alpha, 2.6% beta 146 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 50 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.682A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.609A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.783A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.377A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.642A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.653A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.605A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.750A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.512A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.421A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.543A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.151A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.704A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.274A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.260A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.067A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 400 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 373 hydrogen bonds 746 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1986 1.33 - 1.45: 4368 1.45 - 1.57: 5904 1.57 - 1.69: 585 1.69 - 1.80: 20 Bond restraints: 12863 Sorted by residual: bond pdb=" P B8OG I 55 " pdb=" O5'B8OG I 55 " ideal model delta sigma weight residual 1.708 1.562 0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" C THR B 96 " pdb=" N LEU B 97 " ideal model delta sigma weight residual 1.331 1.274 0.056 1.34e-02 5.57e+03 1.77e+01 bond pdb=" C ARG C 81 " pdb=" N HIS C 82 " ideal model delta sigma weight residual 1.335 1.289 0.046 1.36e-02 5.41e+03 1.15e+01 bond pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.15e+01 bond pdb=" N ASN F 25 " pdb=" CA ASN F 25 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.21e-02 6.83e+03 1.10e+01 ... (remaining 12858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 17527 2.02 - 4.03: 1016 4.03 - 6.05: 67 6.05 - 8.07: 19 8.07 - 10.08: 2 Bond angle restraints: 18631 Sorted by residual: angle pdb=" N LEU F 22 " pdb=" CA LEU F 22 " pdb=" CB LEU F 22 " ideal model delta sigma weight residual 110.65 118.36 -7.71 1.56e+00 4.11e-01 2.44e+01 angle pdb=" N TYR D 121 " pdb=" CA TYR D 121 " pdb=" C TYR D 121 " ideal model delta sigma weight residual 112.38 118.39 -6.01 1.22e+00 6.72e-01 2.43e+01 angle pdb=" N PRO D 50 " pdb=" CA PRO D 50 " pdb=" C PRO D 50 " ideal model delta sigma weight residual 113.81 120.91 -7.10 1.45e+00 4.76e-01 2.40e+01 angle pdb=" N SER D 123 " pdb=" CA SER D 123 " pdb=" C SER D 123 " ideal model delta sigma weight residual 113.19 107.38 5.81 1.19e+00 7.06e-01 2.38e+01 angle pdb=" N GLU G 91 " pdb=" CA GLU G 91 " pdb=" CB GLU G 91 " ideal model delta sigma weight residual 109.82 102.43 7.39 1.52e+00 4.33e-01 2.37e+01 ... (remaining 18626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.84: 5160 28.84 - 57.68: 1705 57.68 - 86.52: 130 86.52 - 115.36: 0 115.36 - 144.20: 4 Dihedral angle restraints: 6999 sinusoidal: 4800 harmonic: 2199 Sorted by residual: dihedral pdb=" CD ARG F 23 " pdb=" NE ARG F 23 " pdb=" CZ ARG F 23 " pdb=" NH1 ARG F 23 " ideal model delta sinusoidal sigma weight residual 0.00 67.94 -67.94 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" CD ARG D 33 " pdb=" NE ARG D 33 " pdb=" CZ ARG D 33 " pdb=" NH1 ARG D 33 " ideal model delta sinusoidal sigma weight residual 0.00 -53.90 53.90 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CD ARG B 23 " pdb=" NE ARG B 23 " pdb=" CZ ARG B 23 " pdb=" NH1 ARG B 23 " ideal model delta sinusoidal sigma weight residual 0.00 -48.95 48.95 1 1.00e+01 1.00e-02 3.29e+01 ... (remaining 6996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 2048 0.122 - 0.244: 65 0.244 - 0.365: 6 0.365 - 0.487: 0 0.487 - 0.609: 1 Chirality restraints: 2120 Sorted by residual: chirality pdb=" P DC I 125 " pdb=" OP1 DC I 125 " pdb=" OP2 DC I 125 " pdb=" O5' DC I 125 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.27e+00 chirality pdb=" CA GLU G 91 " pdb=" N GLU G 91 " pdb=" C GLU G 91 " pdb=" CB GLU G 91 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ARG A 49 " pdb=" N ARG A 49 " pdb=" C ARG A 49 " pdb=" CB ARG A 49 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2117 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 23 " 1.018 9.50e-02 1.11e+02 4.56e-01 1.26e+02 pdb=" NE ARG F 23 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG F 23 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F 23 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 23 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 33 " -0.878 9.50e-02 1.11e+02 3.93e-01 9.40e+01 pdb=" NE ARG D 33 " 0.053 2.00e-02 2.50e+03 pdb=" CZ ARG D 33 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 33 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 33 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 23 " 0.822 9.50e-02 1.11e+02 3.68e-01 8.25e+01 pdb=" NE ARG B 23 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG B 23 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 23 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 23 " 0.023 2.00e-02 2.50e+03 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2198 2.78 - 3.31: 10112 3.31 - 3.84: 24332 3.84 - 4.37: 28469 4.37 - 4.90: 39736 Nonbonded interactions: 104847 Sorted by model distance: nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.253 3.040 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.348 3.040 nonbonded pdb=" O ARG A 49 " pdb=" N ILE A 51 " model vdw 2.354 3.120 nonbonded pdb=" O HIS F 75 " pdb=" NH2 ARG H 92 " model vdw 2.354 3.120 nonbonded pdb=" N7 B8OG I 55 " pdb=" N1 DA J 93 " model vdw 2.379 3.200 ... (remaining 104842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 32 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.370 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 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 : 0.008 0.146 12863 Z= 0.640 Angle : 0.947 10.083 18631 Z= 0.777 Chirality : 0.057 0.609 2120 Planarity : 0.024 0.456 1335 Dihedral : 28.227 144.204 5581 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.30), residues: 743 helix: 1.37 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.92 (0.39), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 71 TYR 0.013 0.002 TYR D 40 PHE 0.010 0.002 PHE E 67 HIS 0.004 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00802 / 0.64 (12863) covalent geometry : angle 0.94651 / 0.78 (18631) hydrogen bonds : bond 0.11308 / 7.38 ( 773) hydrogen bonds : angle 3.95582 / 2.78 ( 1922) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.284 Fit side-chains REVERT: A 129 ARG cc_start: 0.8822 (tpt90) cc_final: 0.8581 (tpt90) REVERT: B 24 ASP cc_start: 0.7520 (t70) cc_final: 0.7176 (t0) REVERT: C 73 ASN cc_start: 0.9058 (t0) cc_final: 0.8362 (t0) REVERT: C 90 ASP cc_start: 0.8499 (t70) cc_final: 0.8222 (t0) REVERT: D 33 ARG cc_start: 0.8187 (mmm-85) cc_final: 0.7980 (ttm110) REVERT: E 59 GLU cc_start: 0.8098 (pm20) cc_final: 0.7809 (pm20) REVERT: E 60 LEU cc_start: 0.8208 (mt) cc_final: 0.7229 (mt) REVERT: F 25 ASN cc_start: 0.8636 (m-40) cc_final: 0.8356 (m-40) REVERT: F 91 LYS cc_start: 0.9169 (ttmt) cc_final: 0.8884 (ttpt) REVERT: G 90 ASP cc_start: 0.8571 (t70) cc_final: 0.8129 (t0) REVERT: H 71 GLU cc_start: 0.8589 (mp0) cc_final: 0.8342 (mt-10) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.8375 time to fit residues: 160.6342 Evaluate side-chains 165 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 38, 61, 45] chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN D 84 ASN E 108 ASN E 125 GLN F 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.086172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.054898 restraints weight = 24044.282| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 1.69 r_work: 0.2569 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2430 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2434 r_free = 0.2434 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2434 r_free = 0.2434 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12863 Z= 0.154 Angle : 0.646 6.704 18631 Z= 0.379 Chirality : 0.044 0.226 2120 Planarity : 0.005 0.054 1335 Dihedral : 30.683 144.843 4077 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.38 % Allowed : 16.32 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.31), residues: 743 helix: 2.17 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.66 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 42 TYR 0.011 0.001 TYR D 40 PHE 0.017 0.001 PHE E 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.15 (12863) covalent geometry : angle 0.64627 / 0.38 (18631) hydrogen bonds : bond 0.04612 / 3.06 ( 773) hydrogen bonds : angle 3.10723 / 2.15 ( 1922) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7653 (t70) cc_final: 0.7309 (t0) REVERT: C 73 ASN cc_start: 0.8894 (t0) cc_final: 0.8193 (t0) REVERT: D 35 GLU cc_start: 0.8491 (mm-30) cc_final: 0.7880 (mm-30) REVERT: E 59 GLU cc_start: 0.8069 (pm20) cc_final: 0.7793 (pm20) REVERT: F 25 ASN cc_start: 0.8796 (m110) cc_final: 0.8432 (m-40) REVERT: F 91 LYS cc_start: 0.9186 (ttmt) cc_final: 0.8889 (ttpt) REVERT: G 90 ASP cc_start: 0.8452 (t70) cc_final: 0.7975 (t0) REVERT: G 92 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8430 (mt-10) REVERT: H 71 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8266 (mt-10) outliers start: 15 outliers final: 4 residues processed: 178 average time/residue: 0.8054 time to fit residues: 151.4373 Evaluate side-chains 172 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [18, 77, 37, 40, 27, 14, 25, 16, 93, 75, 52] chunk 18 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN F 75 HIS H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.085366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.053933 restraints weight = 24458.240| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 1.71 r_work: 0.2545 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2407 r_free = 0.2407 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2407 r_free = 0.2407 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12863 Z= 0.192 Angle : 0.634 6.212 18631 Z= 0.369 Chirality : 0.044 0.240 2120 Planarity : 0.004 0.041 1335 Dihedral : 30.851 145.360 4077 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.01 % Allowed : 16.80 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.31), residues: 743 helix: 2.48 (0.23), residues: 549 sheet: None (None), residues: 0 loop : -0.57 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 86 TYR 0.017 0.001 TYR D 40 PHE 0.015 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.19 (12863) covalent geometry : angle 0.63403 / 0.37 (18631) hydrogen bonds : bond 0.04343 / 2.90 ( 773) hydrogen bonds : angle 2.89175 / 2.00 ( 1922) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7677 (t70) cc_final: 0.7368 (t0) REVERT: C 15 LYS cc_start: 0.8080 (ttpp) cc_final: 0.7851 (ttpp) REVERT: C 73 ASN cc_start: 0.8822 (t0) cc_final: 0.8365 (t160) REVERT: D 35 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7921 (mm-30) REVERT: F 25 ASN cc_start: 0.8800 (m110) cc_final: 0.8424 (m-40) REVERT: F 91 LYS cc_start: 0.9195 (ttmt) cc_final: 0.8987 (ttpp) REVERT: G 90 ASP cc_start: 0.8510 (t70) cc_final: 0.8219 (t0) REVERT: G 92 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8486 (mt-10) REVERT: H 71 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8342 (mt-10) outliers start: 19 outliers final: 8 residues processed: 174 average time/residue: 0.8745 time to fit residues: 160.3429 Evaluate side-chains 174 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [66, 48, 4, 39, 13, 53, 62, 49, 12, 58, 6] chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 0.0070 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.086344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.055296 restraints weight = 24153.455| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 1.68 r_work: 0.2572 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2431 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2434 r_free = 0.2434 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2434 r_free = 0.2434 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12863 Z= 0.137 Angle : 0.614 6.143 18631 Z= 0.359 Chirality : 0.043 0.250 2120 Planarity : 0.004 0.039 1335 Dihedral : 30.853 145.201 4077 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.22 % Allowed : 17.75 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.31), residues: 743 helix: 2.53 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.52 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 71 TYR 0.013 0.001 TYR D 40 PHE 0.014 0.001 PHE E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.14 (12863) covalent geometry : angle 0.61366 / 0.36 (18631) hydrogen bonds : bond 0.04004 / 2.67 ( 773) hydrogen bonds : angle 2.82482 / 1.95 ( 1922) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7642 (t70) cc_final: 0.7321 (t0) REVERT: C 73 ASN cc_start: 0.8782 (t0) cc_final: 0.8324 (t160) REVERT: D 35 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7880 (mm-30) REVERT: E 59 GLU cc_start: 0.8053 (pm20) cc_final: 0.7808 (pm20) REVERT: E 73 GLU cc_start: 0.8803 (tt0) cc_final: 0.8352 (tt0) REVERT: F 25 ASN cc_start: 0.8788 (m110) cc_final: 0.8401 (m-40) REVERT: F 91 LYS cc_start: 0.9194 (ttmt) cc_final: 0.8985 (ttpp) REVERT: G 56 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8528 (tt0) REVERT: H 71 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8320 (mt-10) outliers start: 14 outliers final: 9 residues processed: 171 average time/residue: 0.8448 time to fit residues: 152.4865 Evaluate side-chains 177 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [22, 34, 6, 66, 67, 94, 96, 8, 24, 50, 83] chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 0.0870 chunk 6 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.086315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.055033 restraints weight = 24404.261| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 1.71 r_work: 0.2575 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2435 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 12863 Z= 0.141 Angle : 0.604 6.034 18631 Z= 0.355 Chirality : 0.042 0.257 2120 Planarity : 0.004 0.038 1335 Dihedral : 30.839 145.263 4077 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.54 % Allowed : 17.59 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.31), residues: 743 helix: 2.61 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.45 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 71 TYR 0.012 0.001 TYR D 40 PHE 0.012 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (12863) covalent geometry : angle 0.60361 / 0.36 (18631) hydrogen bonds : bond 0.03839 / 2.56 ( 773) hydrogen bonds : angle 2.76727 / 1.91 ( 1922) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7634 (t70) cc_final: 0.7317 (t0) REVERT: C 73 ASN cc_start: 0.8762 (t0) cc_final: 0.8289 (t160) REVERT: D 35 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7877 (mm-30) REVERT: E 59 GLU cc_start: 0.8049 (pm20) cc_final: 0.7744 (pm20) REVERT: F 25 ASN cc_start: 0.8799 (m110) cc_final: 0.8412 (m-40) REVERT: F 91 LYS cc_start: 0.9202 (ttmt) cc_final: 0.8939 (ttpt) REVERT: G 56 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: H 71 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8339 (mt-10) outliers start: 16 outliers final: 9 residues processed: 171 average time/residue: 0.8262 time to fit residues: 149.5205 Evaluate side-chains 172 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [90, 24, 48, 45, 22, 28, 52, 8, 80, 26, 95] chunk 90 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.086531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.054707 restraints weight = 24390.330| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.77 r_work: 0.2641 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12863 Z= 0.174 Angle : 0.616 6.029 18631 Z= 0.358 Chirality : 0.043 0.264 2120 Planarity : 0.004 0.048 1335 Dihedral : 30.918 145.371 4077 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.69 % Allowed : 18.70 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.31), residues: 743 helix: 2.66 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.39 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 11 TYR 0.011 0.001 TYR D 40 PHE 0.012 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (12863) covalent geometry : angle 0.61624 / 0.36 (18631) hydrogen bonds : bond 0.04020 / 2.69 ( 773) hydrogen bonds : angle 2.73162 / 1.88 ( 1922) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.333 Fit side-chains REVERT: A 59 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7304 (pm20) REVERT: B 24 ASP cc_start: 0.7560 (t70) cc_final: 0.7247 (t0) REVERT: C 73 ASN cc_start: 0.8744 (t0) cc_final: 0.8258 (t160) REVERT: D 35 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7702 (mm-30) REVERT: E 59 GLU cc_start: 0.7968 (pm20) cc_final: 0.7638 (pm20) REVERT: F 25 ASN cc_start: 0.8819 (m110) cc_final: 0.8433 (m-40) REVERT: F 91 LYS cc_start: 0.9153 (ttmt) cc_final: 0.8894 (ttpt) outliers start: 17 outliers final: 9 residues processed: 169 average time/residue: 0.8105 time to fit residues: 144.5794 Evaluate side-chains 171 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [86, 20, 79, 93, 37, 68, 15, 27, 57, 39, 34] chunk 86 optimal weight: 40.0000 chunk 20 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN C 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.086689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.054969 restraints weight = 24209.224| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.76 r_work: 0.2644 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (23 function evaluations) r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12863 Z= 0.159 Angle : 0.621 6.881 18631 Z= 0.359 Chirality : 0.043 0.269 2120 Planarity : 0.004 0.054 1335 Dihedral : 30.931 145.335 4077 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.90 % Allowed : 19.49 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.31), residues: 743 helix: 2.67 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.38 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 11 TYR 0.011 0.001 TYR D 40 PHE 0.012 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (12863) covalent geometry : angle 0.62114 / 0.36 (18631) hydrogen bonds : bond 0.03884 / 2.59 ( 773) hydrogen bonds : angle 2.75415 / 1.89 ( 1922) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.391 Fit side-chains REVERT: A 59 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7272 (pm20) REVERT: B 24 ASP cc_start: 0.7579 (t70) cc_final: 0.7267 (t0) REVERT: C 73 ASN cc_start: 0.8730 (t0) cc_final: 0.8263 (t160) REVERT: D 35 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7706 (mm-30) REVERT: E 59 GLU cc_start: 0.7924 (pm20) cc_final: 0.7603 (pm20) REVERT: F 25 ASN cc_start: 0.8817 (m110) cc_final: 0.8440 (m-40) REVERT: F 91 LYS cc_start: 0.9151 (ttmt) cc_final: 0.8896 (ttpt) outliers start: 12 outliers final: 9 residues processed: 168 average time/residue: 0.8164 time to fit residues: 145.0357 Evaluate side-chains 174 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [59, 4, 36, 93, 3, 55, 49, 16, 81, 94, 45] chunk 59 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.085270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.054084 restraints weight = 24167.829| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.70 r_work: 0.2545 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2404 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2407 r_free = 0.2407 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2407 r_free = 0.2407 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12863 Z= 0.183 Angle : 0.625 6.235 18631 Z= 0.359 Chirality : 0.043 0.276 2120 Planarity : 0.004 0.039 1335 Dihedral : 31.050 145.246 4077 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.06 % Allowed : 19.33 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.31), residues: 743 helix: 2.65 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.011 0.001 TYR B 88 PHE 0.012 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (12863) covalent geometry : angle 0.62457 / 0.36 (18631) hydrogen bonds : bond 0.04033 / 2.70 ( 773) hydrogen bonds : angle 2.76238 / 1.90 ( 1922) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.235 Fit side-chains REVERT: A 59 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: B 24 ASP cc_start: 0.7816 (t70) cc_final: 0.7517 (t0) REVERT: C 73 ASN cc_start: 0.8695 (t0) cc_final: 0.8223 (t160) REVERT: D 35 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7827 (mm-30) REVERT: E 59 GLU cc_start: 0.8104 (pm20) cc_final: 0.7804 (pm20) REVERT: F 25 ASN cc_start: 0.8842 (m110) cc_final: 0.8523 (m-40) REVERT: F 91 LYS cc_start: 0.9207 (ttmt) cc_final: 0.8963 (ttpt) outliers start: 13 outliers final: 7 residues processed: 169 average time/residue: 0.8153 time to fit residues: 145.7352 Evaluate side-chains 171 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 64 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [54, 71, 32, 55, 62, 61, 1, 70, 45, 22, 94] chunk 54 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 0.0030 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.085651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.054643 restraints weight = 24273.914| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 1.68 r_work: 0.2559 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2422 r_free = 0.2422 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2422 r_free = 0.2422 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12863 Z= 0.151 Angle : 0.626 7.126 18631 Z= 0.359 Chirality : 0.043 0.279 2120 Planarity : 0.004 0.039 1335 Dihedral : 31.054 145.150 4077 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.58 % Allowed : 20.29 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.31), residues: 743 helix: 2.65 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.32 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.011 0.001 TYR D 40 PHE 0.012 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (12863) covalent geometry : angle 0.62586 / 0.36 (18631) hydrogen bonds : bond 0.03863 / 2.58 ( 773) hydrogen bonds : angle 2.75546 / 1.89 ( 1922) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.380 Fit side-chains REVERT: B 24 ASP cc_start: 0.7801 (t70) cc_final: 0.7498 (t0) REVERT: C 15 LYS cc_start: 0.8254 (ttpp) cc_final: 0.8043 (ttpp) REVERT: C 73 ASN cc_start: 0.8680 (t0) cc_final: 0.8208 (t160) REVERT: C 110 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8360 (p0) REVERT: D 35 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7822 (mm-30) REVERT: E 59 GLU cc_start: 0.8037 (pm20) cc_final: 0.7761 (pm20) REVERT: F 25 ASN cc_start: 0.8872 (m110) cc_final: 0.8480 (m-40) REVERT: F 91 LYS cc_start: 0.9208 (ttmt) cc_final: 0.8966 (ttpt) outliers start: 10 outliers final: 6 residues processed: 167 average time/residue: 0.8089 time to fit residues: 142.9505 Evaluate side-chains 170 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [34, 65, 5, 31, 46, 47, 71, 40, 93, 96, 79] chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.085802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.054760 restraints weight = 24393.255| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 1.70 r_work: 0.2565 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2426 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2428 r_free = 0.2428 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2428 r_free = 0.2428 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12863 Z= 0.140 Angle : 0.617 7.880 18631 Z= 0.355 Chirality : 0.043 0.282 2120 Planarity : 0.004 0.039 1335 Dihedral : 31.042 145.085 4077 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.27 % Allowed : 20.29 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.31), residues: 743 helix: 2.68 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.31 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.011 0.001 TYR D 40 PHE 0.012 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (12863) covalent geometry : angle 0.61731 / 0.36 (18631) hydrogen bonds : bond 0.03774 / 2.52 ( 773) hydrogen bonds : angle 2.73540 / 1.88 ( 1922) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 0.268 Fit side-chains REVERT: A 59 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7575 (pm20) REVERT: B 24 ASP cc_start: 0.7803 (t70) cc_final: 0.7503 (t0) REVERT: C 73 ASN cc_start: 0.8682 (t0) cc_final: 0.8203 (t160) REVERT: C 110 ASN cc_start: 0.9037 (OUTLIER) cc_final: 0.8363 (p0) REVERT: D 35 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7807 (mm-30) REVERT: E 59 GLU cc_start: 0.8023 (pm20) cc_final: 0.7785 (pm20) REVERT: F 25 ASN cc_start: 0.8872 (m110) cc_final: 0.8487 (m-40) REVERT: F 91 LYS cc_start: 0.9205 (ttmt) cc_final: 0.8962 (ttpt) outliers start: 8 outliers final: 4 residues processed: 165 average time/residue: 0.8230 time to fit residues: 143.7057 Evaluate side-chains 169 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [16, 19, 56, 51, 34, 0, 70, 7, 33, 59, 68] chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.086132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.055000 restraints weight = 24279.803| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 1.70 r_work: 0.2568 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2428 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2430 r_free = 0.2430 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2430 r_free = 0.2430 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12863 Z= 0.152 Angle : 0.613 7.023 18631 Z= 0.354 Chirality : 0.042 0.285 2120 Planarity : 0.004 0.039 1335 Dihedral : 31.033 145.030 4077 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.27 % Allowed : 20.44 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.31), residues: 743 helix: 2.67 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.30 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.011 0.001 TYR D 40 PHE 0.011 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (12863) covalent geometry : angle 0.61317 / 0.35 (18631) hydrogen bonds : bond 0.03754 / 2.51 ( 773) hydrogen bonds : angle 2.72206 / 1.87 ( 1922) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6161.60 seconds wall clock time: 105 minutes 4.42 seconds (6304.42 seconds total)