Starting phenix.real_space_refine on Sat Oct 24 03:03:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10gj_75152/10_2026/10gj_75152.cif Found real_map, /net/cci-nas-00/data/ceres_data/10gj_75152/10_2026/10gj_75152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10gj_75152/10_2026/10gj_75152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10gj_75152/10_2026/10gj_75152.map" model { file = "/net/cci-nas-00/data/ceres_data/10gj_75152/10_2026/10gj_75152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10gj_75152/10_2026/10gj_75152.cif" } resolution = 2.8 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 6621 2.51 5 N 2247 2.21 5 O 2819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 11991 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: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" 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: "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: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} 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: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3034 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 147, 3034 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P B8OG J 13 " occ=0.93 ... (21 atoms not shown) pdb=" O8 B8OG J 13 " occ=0.93 Time building chain proxies: 2.56, per 1000 atoms: 0.21 Number of scatterers: 11991 At special positions: 0 Unit cell: (74.072, 113.866, 116.23, 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 2819 8.00 N 2247 7.00 C 6621 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: 1.05 Conformation dependent library (CDL) restraints added in 391.7 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 72.9% alpha, 2.9% beta 146 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.179A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.585A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.552A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.644A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.386A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (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: 4.169A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.876A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.653A pdb=" N ALA D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.513A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.536A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.792A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.666A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.392A 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: 3.722A 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: 7.178A 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: 6.681A 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: 7.600A 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 'C' and resid 101 through 102 removed outlier: 5.929A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.241A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.156A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 397 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.42 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: 2141 1.33 - 1.45: 4321 1.45 - 1.57: 5738 1.57 - 1.69: 585 1.69 - 1.81: 20 Bond restraints: 12805 Sorted by residual: bond pdb=" P B8OG J 13 " pdb=" O5'B8OG J 13 " ideal model delta sigma weight residual 1.708 1.567 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" N ILE G 79 " pdb=" CA ILE G 79 " ideal model delta sigma weight residual 1.461 1.499 -0.038 8.70e-03 1.32e+04 1.94e+01 bond pdb=" N VAL C 107 " pdb=" CA VAL C 107 " ideal model delta sigma weight residual 1.457 1.496 -0.040 1.15e-02 7.56e+03 1.19e+01 bond pdb=" N LEU E 61 " pdb=" CA LEU E 61 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.15e+01 bond pdb=" N VAL F 81 " pdb=" CA VAL F 81 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.76e+00 ... (remaining 12800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 17011 2.00 - 4.01: 1368 4.01 - 6.01: 152 6.01 - 8.01: 21 8.01 - 10.01: 5 Bond angle restraints: 18557 Sorted by residual: angle pdb=" N ASP E 77 " pdb=" CA ASP E 77 " pdb=" C ASP E 77 " ideal model delta sigma weight residual 111.82 106.08 5.74 1.16e+00 7.43e-01 2.45e+01 angle pdb=" N VAL F 70 " pdb=" CA VAL F 70 " pdb=" C VAL F 70 " ideal model delta sigma weight residual 111.44 104.89 6.55 1.34e+00 5.57e-01 2.39e+01 angle pdb=" N ALA H 58 " pdb=" CA ALA H 58 " pdb=" C ALA H 58 " ideal model delta sigma weight residual 111.71 117.19 -5.48 1.15e+00 7.56e-01 2.27e+01 angle pdb=" N LEU A 48 " pdb=" CA LEU A 48 " pdb=" C LEU A 48 " ideal model delta sigma weight residual 111.82 106.29 5.53 1.16e+00 7.43e-01 2.27e+01 angle pdb=" N ILE C 111 " pdb=" CA ILE C 111 " pdb=" CB ILE C 111 " ideal model delta sigma weight residual 111.39 103.11 8.28 1.74e+00 3.30e-01 2.26e+01 ... (remaining 18552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.70: 5097 28.70 - 57.39: 1707 57.39 - 86.09: 141 86.09 - 114.78: 4 114.78 - 143.47: 4 Dihedral angle restraints: 6953 sinusoidal: 4772 harmonic: 2181 Sorted by residual: 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 -78.42 78.42 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CD ARG E 53 " pdb=" NE ARG E 53 " pdb=" CZ ARG E 53 " pdb=" NH1 ARG E 53 " ideal model delta sinusoidal sigma weight residual 0.00 -73.30 73.30 1 1.00e+01 1.00e-02 6.84e+01 dihedral pdb=" CD ARG H 33 " pdb=" NE ARG H 33 " pdb=" CZ ARG H 33 " pdb=" NH1 ARG H 33 " ideal model delta sinusoidal sigma weight residual 0.00 -68.84 68.84 1 1.00e+01 1.00e-02 6.13e+01 ... (remaining 6950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1821 0.089 - 0.179: 229 0.179 - 0.268: 51 0.268 - 0.358: 9 0.358 - 0.447: 3 Chirality restraints: 2113 Sorted by residual: chirality pdb=" CA ILE C 111 " pdb=" N ILE C 111 " pdb=" C ILE C 111 " pdb=" CB ILE C 111 " both_signs ideal model delta sigma weight residual False 2.43 2.88 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.87 -0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" CA ASN F 25 " pdb=" N ASN F 25 " pdb=" C ASN F 25 " pdb=" CB ASN F 25 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 2110 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 23 " 1.087 9.50e-02 1.11e+02 4.87e-01 1.43e+02 pdb=" NE ARG B 23 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 23 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 23 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 23 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 53 " 1.062 9.50e-02 1.11e+02 4.76e-01 1.37e+02 pdb=" NE ARG E 53 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG E 53 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG E 53 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG E 53 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 33 " 1.035 9.50e-02 1.11e+02 4.64e-01 1.30e+02 pdb=" NE ARG H 33 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG H 33 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 33 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 33 " 0.023 2.00e-02 2.50e+03 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2301 2.79 - 3.32: 10167 3.32 - 3.85: 24494 3.85 - 4.37: 28676 4.37 - 4.90: 39673 Nonbonded interactions: 105311 Sorted by model distance: nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.267 3.040 nonbonded pdb=" O THR G 76 " pdb=" OG1 THR H 52 " model vdw 2.331 3.040 nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.352 3.040 nonbonded pdb=" N6 DA I 135 " pdb=" O6 B8OG J 13 " model vdw 2.379 3.120 nonbonded pdb=" NH1 ARG C 32 " pdb=" OP1 DA I 30 " model vdw 2.387 3.120 ... (remaining 105306 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 22 through 101) } ncs_group { reference = (chain 'C' and resid 12 through 117) selection = chain 'G' } ncs_group { reference = chain 'D' 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=0.93 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: 22.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.130 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:7.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 0.141 12805 Z= 0.668 Angle : 1.095 10.013 18557 Z= 0.885 Chirality : 0.067 0.447 2113 Planarity : 0.034 0.487 1326 Dihedral : 28.315 143.475 5547 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 13.76 % Favored : 86.24 % Cbeta Deviations : 0.28 % 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: -0.48 (0.29), residues: 737 helix: 0.31 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.75 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 71 TYR 0.019 0.002 TYR E 54 PHE 0.014 0.002 PHE E 67 HIS 0.009 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00823 / 0.67 (12805) covalent geometry : angle 1.09494 / 0.89 (18557) hydrogen bonds : bond 0.12144 / 7.99 ( 771) hydrogen bonds : angle 4.58699 / 3.30 ( 1921) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.313 Fit side-chains REVERT: A 124 ILE cc_start: 0.8484 (mt) cc_final: 0.8282 (mt) REVERT: B 91 LYS cc_start: 0.8171 (tttm) cc_final: 0.7838 (ttmt) REVERT: C 73 ASN cc_start: 0.8620 (t0) cc_final: 0.8313 (t0) REVERT: D 46 LYS cc_start: 0.7420 (mtmt) cc_final: 0.7063 (mmtp) REVERT: D 85 LYS cc_start: 0.9079 (mttp) cc_final: 0.8658 (mmtt) REVERT: E 129 ARG cc_start: 0.8780 (ttt-90) cc_final: 0.8175 (tpt90) REVERT: G 74 LYS cc_start: 0.9284 (mttt) cc_final: 0.8927 (mtmm) REVERT: G 90 ASP cc_start: 0.8156 (t70) cc_final: 0.7652 (t0) REVERT: G 99 LYS cc_start: 0.8158 (mttt) cc_final: 0.7936 (mtpp) REVERT: H 76 GLU cc_start: 0.8581 (tp30) cc_final: 0.8275 (tp30) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.7552 time to fit residues: 157.6962 Evaluate side-chains 142 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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: 0.8980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN F 64 ASN G 68 ASN H 63 ASN H 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.111857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.072818 restraints weight = 22394.591| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.73 r_work: 0.2908 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12805 Z= 0.160 Angle : 0.652 6.581 18557 Z= 0.384 Chirality : 0.044 0.235 2113 Planarity : 0.006 0.062 1326 Dihedral : 30.648 144.883 4064 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.00 % Allowed : 22.40 % Favored : 73.60 % 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: 1.34 (0.30), residues: 737 helix: 1.57 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -1.08 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 23 TYR 0.011 0.001 TYR F 51 PHE 0.013 0.001 PHE E 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 (12805) covalent geometry : angle 0.65194 / 0.38 (18557) hydrogen bonds : bond 0.04516 / 3.02 ( 771) hydrogen bonds : angle 3.11300 / 2.24 ( 1921) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.319 Fit side-chains REVERT: B 91 LYS cc_start: 0.8850 (tttm) cc_final: 0.8512 (ttmt) REVERT: C 13 LYS cc_start: 0.9034 (mmmt) cc_final: 0.8806 (tmtt) REVERT: C 17 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7900 (mtm180) REVERT: D 35 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: D 82 HIS cc_start: 0.8652 (t-90) cc_final: 0.8451 (t70) REVERT: D 85 LYS cc_start: 0.9210 (mttp) cc_final: 0.8936 (mmtt) REVERT: D 108 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8323 (tptt) REVERT: E 129 ARG cc_start: 0.8769 (ttt-90) cc_final: 0.8530 (tpt90) REVERT: G 29 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7513 (ttm110) REVERT: G 74 LYS cc_start: 0.9369 (mttt) cc_final: 0.9081 (mtmt) REVERT: G 90 ASP cc_start: 0.8068 (t70) cc_final: 0.7747 (t0) REVERT: G 99 LYS cc_start: 0.8437 (mttt) cc_final: 0.8233 (mtpp) REVERT: G 104 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8586 (mm110) REVERT: H 47 GLN cc_start: 0.8807 (tt0) cc_final: 0.8593 (tt0) REVERT: H 63 ASN cc_start: 0.8468 (t0) cc_final: 0.8239 (t0) outliers start: 25 outliers final: 3 residues processed: 165 average time/residue: 0.7719 time to fit residues: 134.8440 Evaluate side-chains 147 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 29 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [88, 77, 35, 10, 41, 7, 21, 22, 54, 43, 42] chunk 88 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 64 ASN H 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.111399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.072129 restraints weight = 22878.082| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.75 r_work: 0.2901 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12805 Z= 0.147 Angle : 0.600 6.360 18557 Z= 0.358 Chirality : 0.042 0.285 2113 Planarity : 0.005 0.048 1326 Dihedral : 30.815 143.517 4064 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.84 % Allowed : 23.68 % Favored : 72.48 % 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: 2.31 (0.30), residues: 737 helix: 2.27 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.72 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 33 TYR 0.012 0.002 TYR H 83 PHE 0.011 0.001 PHE E 67 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.15 (12805) covalent geometry : angle 0.59950 / 0.36 (18557) hydrogen bonds : bond 0.04063 / 2.71 ( 771) hydrogen bonds : angle 2.77620 / 2.02 ( 1921) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.336 Fit side-chains REVERT: B 91 LYS cc_start: 0.9001 (tttm) cc_final: 0.8693 (ttmt) REVERT: C 56 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: D 35 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7586 (mt-10) REVERT: D 85 LYS cc_start: 0.9273 (mttp) cc_final: 0.9001 (mmtt) REVERT: E 129 ARG cc_start: 0.8804 (ttt-90) cc_final: 0.8579 (tpt90) REVERT: F 27 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8264 (mp10) REVERT: G 29 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7552 (ttm110) REVERT: G 74 LYS cc_start: 0.9375 (mttt) cc_final: 0.9092 (mtmt) REVERT: G 84 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: G 99 LYS cc_start: 0.8535 (mttt) cc_final: 0.8297 (mtpp) REVERT: G 104 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8572 (mm110) REVERT: H 68 ASP cc_start: 0.9165 (t0) cc_final: 0.8928 (t0) REVERT: H 85 LYS cc_start: 0.9038 (mmtm) cc_final: 0.8833 (mmtm) outliers start: 24 outliers final: 4 residues processed: 160 average time/residue: 0.7509 time to fit residues: 127.3817 Evaluate side-chains 152 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 84 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [87, 48, 19, 56, 14, 12, 31, 57, 83, 49, 84] chunk 87 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN E 108 ASN G 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.109951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.070437 restraints weight = 22592.959| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.74 r_work: 0.2864 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12805 Z= 0.162 Angle : 0.619 9.335 18557 Z= 0.358 Chirality : 0.041 0.285 2113 Planarity : 0.005 0.050 1326 Dihedral : 30.944 142.294 4064 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.04 % Allowed : 24.16 % Favored : 72.80 % 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 (0.30), residues: 737 helix: 2.47 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.60 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 33 TYR 0.011 0.001 TYR E 54 PHE 0.008 0.001 PHE E 67 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (12805) covalent geometry : angle 0.61876 / 0.36 (18557) hydrogen bonds : bond 0.03957 / 2.62 ( 771) hydrogen bonds : angle 2.70165 / 1.95 ( 1921) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9276 (m-30) cc_final: 0.8951 (m-30) REVERT: B 91 LYS cc_start: 0.9016 (tttm) cc_final: 0.8724 (ttmt) REVERT: D 85 LYS cc_start: 0.9345 (mttp) cc_final: 0.9055 (mmtt) REVERT: E 50 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8591 (mp0) REVERT: G 74 LYS cc_start: 0.9353 (mttt) cc_final: 0.9081 (mtmt) REVERT: G 99 LYS cc_start: 0.8668 (mttt) cc_final: 0.8444 (mtpp) REVERT: G 104 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8677 (mm110) REVERT: H 68 ASP cc_start: 0.9203 (t0) cc_final: 0.8917 (t0) REVERT: H 85 LYS cc_start: 0.9171 (mmtm) cc_final: 0.8937 (mmtm) outliers start: 19 outliers final: 5 residues processed: 165 average time/residue: 0.7772 time to fit residues: 135.7156 Evaluate side-chains 153 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [13, 54, 63, 71, 28, 25, 32, 21, 6, 35, 88] chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.109252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.070008 restraints weight = 22840.959| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.83 r_work: 0.2853 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12805 Z= 0.143 Angle : 0.581 6.777 18557 Z= 0.344 Chirality : 0.041 0.307 2113 Planarity : 0.004 0.063 1326 Dihedral : 30.907 143.170 4064 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.36 % Allowed : 24.16 % Favored : 72.48 % 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: 2.82 (0.31), residues: 737 helix: 2.62 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.49 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 33 TYR 0.013 0.001 TYR E 54 PHE 0.008 0.001 PHE E 67 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (12805) covalent geometry : angle 0.58100 / 0.34 (18557) hydrogen bonds : bond 0.03856 / 2.56 ( 771) hydrogen bonds : angle 2.65084 / 1.92 ( 1921) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.312 Fit side-chains REVERT: A 123 ASP cc_start: 0.9101 (m-30) cc_final: 0.8845 (m-30) REVERT: B 35 ARG cc_start: 0.8038 (mtp85) cc_final: 0.7341 (mtp85) REVERT: B 91 LYS cc_start: 0.8749 (tttm) cc_final: 0.8450 (ttmt) REVERT: B 93 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6950 (mp10) REVERT: D 35 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: D 85 LYS cc_start: 0.9306 (mttp) cc_final: 0.8887 (mmtt) REVERT: G 74 LYS cc_start: 0.9252 (mttt) cc_final: 0.8940 (mtmt) REVERT: G 99 LYS cc_start: 0.8398 (mttt) cc_final: 0.8147 (mtpp) REVERT: G 104 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8448 (mm110) REVERT: H 68 ASP cc_start: 0.8935 (t0) cc_final: 0.8610 (t0) REVERT: H 85 LYS cc_start: 0.9027 (mmtm) cc_final: 0.8775 (mmtm) outliers start: 21 outliers final: 7 residues processed: 162 average time/residue: 0.7971 time to fit residues: 136.3635 Evaluate side-chains 155 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [39, 46, 74, 54, 94, 52, 79, 87, 8, 30, 16] chunk 39 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN C 94 ASN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.108935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.069460 restraints weight = 22827.679| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.85 r_work: 0.2838 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12805 Z= 0.143 Angle : 0.585 8.965 18557 Z= 0.343 Chirality : 0.040 0.296 2113 Planarity : 0.005 0.107 1326 Dihedral : 30.901 142.727 4064 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.52 % Allowed : 23.36 % Favored : 73.12 % 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: 737 helix: 2.66 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.47 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 71 TYR 0.015 0.001 TYR E 54 PHE 0.006 0.001 PHE A 67 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (12805) covalent geometry : angle 0.58511 / 0.34 (18557) hydrogen bonds : bond 0.03798 / 2.54 ( 771) hydrogen bonds : angle 2.60285 / 1.88 ( 1921) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.327 Fit side-chains REVERT: A 123 ASP cc_start: 0.9094 (m-30) cc_final: 0.8669 (m-30) REVERT: B 91 LYS cc_start: 0.8777 (tttm) cc_final: 0.8509 (ttmt) REVERT: D 85 LYS cc_start: 0.9324 (mttp) cc_final: 0.8902 (mmtt) REVERT: D 108 LYS cc_start: 0.8364 (ttmm) cc_final: 0.7862 (tttm) REVERT: D 113 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7717 (mp0) REVERT: G 74 LYS cc_start: 0.9233 (mttt) cc_final: 0.8937 (mtmt) REVERT: G 99 LYS cc_start: 0.8421 (mttt) cc_final: 0.8147 (mtpp) REVERT: H 63 ASN cc_start: 0.8080 (t0) cc_final: 0.7607 (m-40) REVERT: H 68 ASP cc_start: 0.8920 (t0) cc_final: 0.8590 (t0) REVERT: H 85 LYS cc_start: 0.9061 (mmtm) cc_final: 0.8818 (mmtm) outliers start: 22 outliers final: 8 residues processed: 161 average time/residue: 0.8526 time to fit residues: 144.8640 Evaluate side-chains 157 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [28, 79, 59, 12, 77, 27, 67, 6, 89, 66, 35] chunk 28 optimal weight: 0.4980 chunk 79 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.107143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.067640 restraints weight = 22189.929| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.69 r_work: 0.2800 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12805 Z= 0.195 Angle : 0.635 7.080 18557 Z= 0.362 Chirality : 0.043 0.317 2113 Planarity : 0.005 0.121 1326 Dihedral : 31.064 142.566 4064 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.84 % Allowed : 24.48 % Favored : 71.68 % 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: 2.71 (0.31), residues: 737 helix: 2.54 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.54 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 33 TYR 0.014 0.001 TYR E 54 PHE 0.009 0.002 PHE F 100 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.20 (12805) covalent geometry : angle 0.63475 / 0.36 (18557) hydrogen bonds : bond 0.04445 / 2.94 ( 771) hydrogen bonds : angle 2.76639 / 2.00 ( 1921) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.334 Fit side-chains REVERT: A 123 ASP cc_start: 0.9195 (m-30) cc_final: 0.8983 (m-30) REVERT: D 35 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: D 46 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8578 (mptm) REVERT: D 85 LYS cc_start: 0.9408 (mttp) cc_final: 0.9089 (mmtt) REVERT: D 90 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8148 (p) REVERT: E 96 SER cc_start: 0.9123 (m) cc_final: 0.8916 (m) REVERT: F 27 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8450 (mp10) REVERT: G 74 LYS cc_start: 0.9304 (mttt) cc_final: 0.9050 (mtmt) REVERT: G 81 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8531 (tpt170) REVERT: G 99 LYS cc_start: 0.8703 (mttt) cc_final: 0.8416 (mtpp) REVERT: G 104 GLN cc_start: 0.8993 (tp40) cc_final: 0.8765 (mm110) REVERT: H 63 ASN cc_start: 0.8418 (t0) cc_final: 0.7968 (m-40) REVERT: H 68 ASP cc_start: 0.9209 (t0) cc_final: 0.8879 (t0) REVERT: H 85 LYS cc_start: 0.9272 (mmtm) cc_final: 0.9050 (mmtm) outliers start: 24 outliers final: 9 residues processed: 170 average time/residue: 0.8541 time to fit residues: 152.8622 Evaluate side-chains 168 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 81 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [96, 12, 13, 17, 49, 78, 22, 98, 73, 71, 42] chunk 96 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 98 optimal weight: 20.0000 chunk 73 optimal weight: 40.0000 chunk 71 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.107840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.068314 restraints weight = 22261.818| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.73 r_work: 0.2811 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12805 Z= 0.150 Angle : 0.602 9.399 18557 Z= 0.347 Chirality : 0.041 0.313 2113 Planarity : 0.004 0.050 1326 Dihedral : 30.999 142.677 4064 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.24 % Allowed : 25.76 % Favored : 72.00 % 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: 2.82 (0.31), residues: 737 helix: 2.64 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.54 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 71 TYR 0.013 0.001 TYR E 54 PHE 0.006 0.001 PHE A 67 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (12805) covalent geometry : angle 0.60235 / 0.35 (18557) hydrogen bonds : bond 0.03844 / 2.57 ( 771) hydrogen bonds : angle 2.67821 / 1.93 ( 1921) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.330 Fit side-chains REVERT: A 120 MET cc_start: 0.8783 (mtp) cc_final: 0.8394 (mtp) REVERT: A 123 ASP cc_start: 0.9191 (m-30) cc_final: 0.8981 (m-30) REVERT: D 85 LYS cc_start: 0.9403 (mttp) cc_final: 0.9078 (mmtt) REVERT: D 108 LYS cc_start: 0.8616 (ttmm) cc_final: 0.8103 (tttm) REVERT: G 74 LYS cc_start: 0.9277 (mttt) cc_final: 0.9025 (mtmt) REVERT: G 81 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8493 (tpt170) REVERT: G 99 LYS cc_start: 0.8703 (mttt) cc_final: 0.8428 (mtpp) REVERT: H 63 ASN cc_start: 0.8418 (t0) cc_final: 0.7986 (m-40) REVERT: H 68 ASP cc_start: 0.9189 (t0) cc_final: 0.8895 (t0) REVERT: H 85 LYS cc_start: 0.9252 (mmtm) cc_final: 0.9041 (mmtm) outliers start: 14 outliers final: 5 residues processed: 165 average time/residue: 0.8288 time to fit residues: 144.2124 Evaluate side-chains 162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 156 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 81 ARG Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [6, 73, 90, 37, 31, 39, 36, 23, 81, 55, 78] chunk 6 optimal weight: 1.9990 chunk 73 optimal weight: 40.0000 chunk 90 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN B 25 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.104042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.064100 restraints weight = 22417.388| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.80 r_work: 0.2733 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12805 Z= 0.261 Angle : 0.696 9.126 18557 Z= 0.384 Chirality : 0.047 0.323 2113 Planarity : 0.005 0.065 1326 Dihedral : 31.290 143.022 4064 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.24 % Allowed : 26.08 % Favored : 71.68 % 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: 2.37 (0.30), residues: 737 helix: 2.32 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.75 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 33 TYR 0.015 0.002 TYR E 54 PHE 0.011 0.002 PHE F 100 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.26 (12805) covalent geometry : angle 0.69593 / 0.38 (18557) hydrogen bonds : bond 0.05058 / 3.37 ( 771) hydrogen bonds : angle 2.87575 / 2.07 ( 1921) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9093 (m-30) cc_final: 0.8851 (m-30) REVERT: D 85 LYS cc_start: 0.9331 (mttp) cc_final: 0.8898 (mmtt) REVERT: D 90 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7687 (p) REVERT: D 108 LYS cc_start: 0.8422 (ttmm) cc_final: 0.7906 (tttm) REVERT: G 74 LYS cc_start: 0.9158 (mttt) cc_final: 0.8917 (mtmt) REVERT: G 81 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8228 (tpt170) REVERT: G 91 GLU cc_start: 0.8498 (tp30) cc_final: 0.8296 (tp30) REVERT: G 95 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8568 (tmtt) REVERT: G 99 LYS cc_start: 0.8463 (mttt) cc_final: 0.8224 (mttm) REVERT: H 63 ASN cc_start: 0.8085 (t0) cc_final: 0.7589 (m-40) REVERT: H 68 ASP cc_start: 0.8942 (t0) cc_final: 0.8587 (t0) REVERT: H 85 LYS cc_start: 0.9157 (mmtm) cc_final: 0.8912 (mmtm) outliers start: 14 outliers final: 5 residues processed: 167 average time/residue: 0.8241 time to fit residues: 145.0673 Evaluate side-chains 160 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 81 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [41, 65, 9, 77, 12, 8, 56, 14, 50, 93, 61] chunk 41 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.106271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.066443 restraints weight = 22838.253| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.83 r_work: 0.2765 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12805 Z= 0.141 Angle : 0.635 11.143 18557 Z= 0.359 Chirality : 0.043 0.332 2113 Planarity : 0.004 0.063 1326 Dihedral : 31.173 143.045 4064 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.44 % Allowed : 28.00 % Favored : 70.56 % 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: 2.65 (0.31), residues: 737 helix: 2.55 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.73 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 71 TYR 0.011 0.001 TYR E 54 PHE 0.005 0.001 PHE B 61 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (12805) covalent geometry : angle 0.63465 / 0.36 (18557) hydrogen bonds : bond 0.03832 / 2.55 ( 771) hydrogen bonds : angle 2.72674 / 1.97 ( 1921) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9086 (m-30) cc_final: 0.8859 (m-30) REVERT: B 25 ASN cc_start: 0.8581 (m110) cc_final: 0.8260 (m-40) REVERT: D 85 LYS cc_start: 0.9351 (mttp) cc_final: 0.8937 (mmtt) REVERT: D 90 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7736 (p) REVERT: D 105 GLU cc_start: 0.8583 (tp30) cc_final: 0.8309 (tp30) REVERT: D 108 LYS cc_start: 0.8410 (ttmm) cc_final: 0.7915 (tttm) REVERT: G 74 LYS cc_start: 0.9166 (mttt) cc_final: 0.8936 (mtmt) REVERT: G 99 LYS cc_start: 0.8477 (mttt) cc_final: 0.8175 (mtpp) REVERT: H 63 ASN cc_start: 0.8111 (t0) cc_final: 0.7642 (m-40) REVERT: H 68 ASP cc_start: 0.8977 (t0) cc_final: 0.8633 (t0) REVERT: H 85 LYS cc_start: 0.9169 (mmtm) cc_final: 0.8941 (mmtm) outliers start: 9 outliers final: 4 residues processed: 163 average time/residue: 0.8425 time to fit residues: 144.7002 Evaluate side-chains 156 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [33, 28, 54, 5, 36, 87, 88, 61, 39, 94, 72] chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 0.0770 chunk 5 optimal weight: 0.2980 chunk 36 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 72 optimal weight: 50.0000 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 125 GLN G 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.106679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.067292 restraints weight = 22583.895| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.84 r_work: 0.2748 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12805 Z= 0.136 Angle : 0.614 10.893 18557 Z= 0.353 Chirality : 0.041 0.325 2113 Planarity : 0.005 0.080 1326 Dihedral : 31.007 142.931 4064 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.76 % Allowed : 27.52 % Favored : 70.72 % 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: 2.82 (0.31), residues: 737 helix: 2.66 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.63 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 71 TYR 0.015 0.001 TYR E 54 PHE 0.007 0.001 PHE A 67 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (12805) covalent geometry : angle 0.61431 / 0.35 (18557) hydrogen bonds : bond 0.03757 / 2.52 ( 771) hydrogen bonds : angle 2.66251 / 1.92 ( 1921) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4420.49 seconds wall clock time: 75 minutes 52.22 seconds (4552.22 seconds total)