Starting phenix.real_space_refine on Wed May 14 08:36:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kb5_37070/05_2025/8kb5_37070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kb5_37070/05_2025/8kb5_37070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26133 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kb5_37070/05_2025/8kb5_37070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kb5_37070/05_2025/8kb5_37070.map" model { file = "/net/cci-nas-00/data/ceres_data/8kb5_37070/05_2025/8kb5_37070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kb5_37070/05_2025/8kb5_37070.cif" } resolution = 2.26133 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 288 5.49 5 S 10 5.16 5 C 6610 2.51 5 N 2249 2.21 5 O 2796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11953 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2970 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2969 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 7.51, per 1000 atoms: 0.63 Number of scatterers: 11953 At special positions: 0 Unit cell: (117.66, 96.46, 118.72, 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 288 15.00 O 2796 8.00 N 2249 7.00 C 6610 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: 2.87 Conformation dependent library (CDL) restraints added in 980.2 milliseconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1408 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.1% alpha, 2.9% beta 144 base pairs and 261 stacking pairs defined. Time for finding SS restraints: 5.92 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.148A 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 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: 3.685A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (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 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.501A 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 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.705A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (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 131 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: 3.766A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 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: 4.349A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 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 104 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.871A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.125A 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 100 through 102 removed outlier: 6.673A 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: 7.032A 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: 7.071A 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 78 412 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 261 stacking parallelities Total time for adding SS restraints: 4.44 Time building geometry restraints manager: 3.38 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: 2323 1.33 - 1.46: 4297 1.46 - 1.58: 5543 1.58 - 1.70: 577 1.70 - 1.82: 18 Bond restraints: 12758 Sorted by residual: bond pdb=" CA GLN F 93 " pdb=" C GLN F 93 " ideal model delta sigma weight residual 1.522 1.590 -0.068 1.38e-02 5.25e+03 2.43e+01 bond pdb=" CZ ARG A 134 " pdb=" NH2 ARG A 134 " ideal model delta sigma weight residual 1.330 1.281 0.049 1.30e-02 5.92e+03 1.45e+01 bond pdb=" CZ ARG G 32 " pdb=" NH2 ARG G 32 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" CZ ARG C 32 " pdb=" NH2 ARG C 32 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" CZ ARG B 95 " pdb=" NH2 ARG B 95 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.00e+01 ... (remaining 12753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 16896 1.68 - 3.35: 1286 3.35 - 5.03: 247 5.03 - 6.71: 42 6.71 - 8.38: 8 Bond angle restraints: 18479 Sorted by residual: angle pdb=" N GLN F 93 " pdb=" CA GLN F 93 " pdb=" C GLN F 93 " ideal model delta sigma weight residual 113.01 106.29 6.72 1.20e+00 6.94e-01 3.14e+01 angle pdb=" C ARG B 92 " pdb=" CA ARG B 92 " pdb=" CB ARG B 92 " ideal model delta sigma weight residual 110.88 103.22 7.66 1.57e+00 4.06e-01 2.38e+01 angle pdb=" N VAL F 87 " pdb=" CA VAL F 87 " pdb=" C VAL F 87 " ideal model delta sigma weight residual 110.72 105.89 4.83 1.01e+00 9.80e-01 2.28e+01 angle pdb=" C HIS A 39 " pdb=" N ARG A 40 " pdb=" CA ARG A 40 " ideal model delta sigma weight residual 120.82 127.54 -6.72 1.41e+00 5.03e-01 2.27e+01 angle pdb=" C ARG A 40 " pdb=" N TYR A 41 " pdb=" CA TYR A 41 " ideal model delta sigma weight residual 120.87 126.97 -6.10 1.42e+00 4.96e-01 1.85e+01 ... (remaining 18474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4327 17.62 - 35.24: 1141 35.24 - 52.86: 1073 52.86 - 70.48: 343 70.48 - 88.11: 16 Dihedral angle restraints: 6900 sinusoidal: 4712 harmonic: 2188 Sorted by residual: dihedral pdb=" CA PHE A 84 " pdb=" C PHE A 84 " pdb=" N GLN A 85 " pdb=" CA GLN A 85 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" N GLN A 76 " pdb=" C GLN A 76 " pdb=" CA GLN A 76 " pdb=" CB GLN A 76 " ideal model delta harmonic sigma weight residual 122.80 131.80 -9.00 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 162.15 17.85 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 6897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1983 0.097 - 0.194: 111 0.194 - 0.291: 7 0.291 - 0.388: 2 0.388 - 0.485: 1 Chirality restraints: 2104 Sorted by residual: chirality pdb=" P DT I -17 " pdb=" OP1 DT I -17 " pdb=" OP2 DT I -17 " pdb=" O5' DT I -17 " both_signs ideal model delta sigma weight residual True 2.35 -2.83 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C4' DC I 49 " pdb=" C5' DC I 49 " pdb=" O4' DC I 49 " pdb=" C3' DC I 49 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA GLN A 76 " pdb=" N GLN A 76 " pdb=" C GLN A 76 " pdb=" CB GLN A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 2101 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 56 " 0.119 2.00e-02 2.50e+03 6.39e-02 1.22e+02 pdb=" N9 DG J 56 " 0.033 2.00e-02 2.50e+03 pdb=" C8 DG J 56 " -0.095 2.00e-02 2.50e+03 pdb=" N7 DG J 56 " -0.092 2.00e-02 2.50e+03 pdb=" C5 DG J 56 " -0.010 2.00e-02 2.50e+03 pdb=" C6 DG J 56 " 0.041 2.00e-02 2.50e+03 pdb=" O6 DG J 56 " 0.088 2.00e-02 2.50e+03 pdb=" N1 DG J 56 " 0.030 2.00e-02 2.50e+03 pdb=" C2 DG J 56 " -0.022 2.00e-02 2.50e+03 pdb=" N2 DG J 56 " -0.069 2.00e-02 2.50e+03 pdb=" N3 DG J 56 " -0.019 2.00e-02 2.50e+03 pdb=" C4 DG J 56 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I -47 " 0.091 2.00e-02 2.50e+03 6.55e-02 1.07e+02 pdb=" N1 DT I -47 " 0.042 2.00e-02 2.50e+03 pdb=" C2 DT I -47 " -0.016 2.00e-02 2.50e+03 pdb=" O2 DT I -47 " -0.122 2.00e-02 2.50e+03 pdb=" N3 DT I -47 " 0.015 2.00e-02 2.50e+03 pdb=" C4 DT I -47 " 0.026 2.00e-02 2.50e+03 pdb=" O4 DT I -47 " 0.092 2.00e-02 2.50e+03 pdb=" C5 DT I -47 " -0.028 2.00e-02 2.50e+03 pdb=" C7 DT I -47 " -0.086 2.00e-02 2.50e+03 pdb=" C6 DT I -47 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 59 " 0.120 2.00e-02 2.50e+03 6.05e-02 1.01e+02 pdb=" N9 DA I 59 " 0.007 2.00e-02 2.50e+03 pdb=" C8 DA I 59 " -0.070 2.00e-02 2.50e+03 pdb=" N7 DA I 59 " -0.062 2.00e-02 2.50e+03 pdb=" C5 DA I 59 " -0.019 2.00e-02 2.50e+03 pdb=" C6 DA I 59 " 0.017 2.00e-02 2.50e+03 pdb=" N6 DA I 59 " 0.115 2.00e-02 2.50e+03 pdb=" N1 DA I 59 " -0.023 2.00e-02 2.50e+03 pdb=" C2 DA I 59 " -0.041 2.00e-02 2.50e+03 pdb=" N3 DA I 59 " -0.026 2.00e-02 2.50e+03 pdb=" C4 DA I 59 " -0.017 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 3664 2.88 - 3.39: 10210 3.39 - 3.89: 24290 3.89 - 4.40: 27833 4.40 - 4.90: 37547 Nonbonded interactions: 103544 Sorted by model distance: nonbonded pdb=" NE2 GLN E 125 " pdb=" OE2 GLU F 53 " model vdw 2.377 3.120 nonbonded pdb=" O ALA E 114 " pdb=" OG1 THR E 115 " model vdw 2.400 3.040 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.457 3.040 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.488 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NE ARG E 131 " model vdw 2.508 3.120 ... (remaining 103539 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' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid -72 through -1 or resid 1 through 72)) selection = (chain 'J' and (resid -72 through -1 or resid 1 through 72)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.800 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 12758 Z= 0.369 Angle : 0.975 8.383 18479 Z= 0.624 Chirality : 0.049 0.485 2104 Planarity : 0.013 0.111 1336 Dihedral : 28.085 88.105 5492 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.29), residues: 742 helix: 1.97 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -0.07 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.020 0.003 HIS E 39 PHE 0.029 0.003 PHE F 100 TYR 0.110 0.004 TYR F 51 ARG 0.012 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.11620 ( 782) hydrogen bonds : angle 3.68069 ( 1952) covalent geometry : bond 0.00674 (12758) covalent geometry : angle 0.97520 (18479) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.885 Fit side-chains REVERT: C 61 GLU cc_start: 0.8294 (tp30) cc_final: 0.8078 (tp30) REVERT: C 99 ARG cc_start: 0.7357 (mmt180) cc_final: 0.7056 (mmm160) REVERT: D 36 SER cc_start: 0.8427 (p) cc_final: 0.8201 (p) REVERT: D 46 LYS cc_start: 0.8907 (mmpt) cc_final: 0.8586 (mmmt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 2.1658 time to fit residues: 360.2376 Evaluate side-chains 148 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN D 63 ASN D 84 ASN F 93 GLN G 24 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.164993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124401 restraints weight = 9964.647| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 0.91 r_work: 0.3241 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12758 Z= 0.227 Angle : 0.626 8.380 18479 Z= 0.379 Chirality : 0.039 0.197 2104 Planarity : 0.005 0.043 1336 Dihedral : 30.538 74.009 4006 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.43 % Allowed : 13.54 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.30), residues: 742 helix: 2.30 (0.21), residues: 554 sheet: None (None), residues: 0 loop : 0.00 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 75 PHE 0.014 0.002 PHE E 67 TYR 0.015 0.002 TYR F 51 ARG 0.005 0.001 ARG H 92 Details of bonding type rmsd hydrogen bonds : bond 0.05830 ( 782) hydrogen bonds : angle 3.02962 ( 1952) covalent geometry : bond 0.00494 (12758) covalent geometry : angle 0.62636 (18479) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8129 (tp30) cc_final: 0.7909 (tp30) REVERT: C 71 ARG cc_start: 0.7198 (ttm110) cc_final: 0.6989 (ttp80) REVERT: C 99 ARG cc_start: 0.7800 (mmt180) cc_final: 0.7323 (mmm160) REVERT: G 15 LYS cc_start: 0.8002 (mtpm) cc_final: 0.7614 (mtmt) outliers start: 9 outliers final: 3 residues processed: 161 average time/residue: 2.0937 time to fit residues: 352.9934 Evaluate side-chains 158 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 24 GLN C 104 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.164441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124877 restraints weight = 10115.582| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 0.93 r_work: 0.3223 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12758 Z= 0.239 Angle : 0.635 8.726 18479 Z= 0.383 Chirality : 0.040 0.174 2104 Planarity : 0.005 0.044 1336 Dihedral : 30.589 74.394 4006 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.07 % Allowed : 13.54 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.30), residues: 742 helix: 2.29 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.02 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 75 PHE 0.014 0.002 PHE E 67 TYR 0.017 0.002 TYR H 83 ARG 0.006 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.05985 ( 782) hydrogen bonds : angle 3.01849 ( 1952) covalent geometry : bond 0.00523 (12758) covalent geometry : angle 0.63522 (18479) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.921 Fit side-chains REVERT: C 99 ARG cc_start: 0.7871 (mmt180) cc_final: 0.7380 (mmm160) REVERT: E 59 GLU cc_start: 0.8512 (pm20) cc_final: 0.8005 (pm20) REVERT: F 79 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8759 (mtmt) REVERT: G 15 LYS cc_start: 0.8069 (mtpm) cc_final: 0.7671 (mtmt) outliers start: 13 outliers final: 6 residues processed: 160 average time/residue: 2.0297 time to fit residues: 340.3177 Evaluate side-chains 160 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 56 optimal weight: 0.0470 chunk 34 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 23 optimal weight: 0.0030 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.9690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 112 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.166058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.126463 restraints weight = 9962.703| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 0.92 r_work: 0.3245 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12758 Z= 0.181 Angle : 0.598 8.043 18479 Z= 0.365 Chirality : 0.036 0.160 2104 Planarity : 0.005 0.041 1336 Dihedral : 30.569 74.170 4006 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.75 % Allowed : 14.49 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.30), residues: 742 helix: 2.45 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.03 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.013 0.002 PHE E 67 TYR 0.016 0.002 TYR H 83 ARG 0.012 0.000 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.05339 ( 782) hydrogen bonds : angle 2.97673 ( 1952) covalent geometry : bond 0.00383 (12758) covalent geometry : angle 0.59831 (18479) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.849 Fit side-chains REVERT: C 99 ARG cc_start: 0.7866 (mmt180) cc_final: 0.7371 (mmm160) REVERT: E 59 GLU cc_start: 0.8470 (pm20) cc_final: 0.7957 (pm20) REVERT: E 86 ARG cc_start: 0.7850 (ttt180) cc_final: 0.7623 (tpt170) REVERT: F 79 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8750 (mtmt) REVERT: G 15 LYS cc_start: 0.8021 (mtpm) cc_final: 0.7644 (mtmt) outliers start: 11 outliers final: 5 residues processed: 157 average time/residue: 2.0327 time to fit residues: 334.6022 Evaluate side-chains 157 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 151 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 79 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.0670 chunk 96 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.166129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126539 restraints weight = 10046.982| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 0.94 r_work: 0.3246 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12758 Z= 0.196 Angle : 0.594 7.964 18479 Z= 0.362 Chirality : 0.037 0.163 2104 Planarity : 0.005 0.056 1336 Dihedral : 30.495 73.867 4006 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.91 % Allowed : 14.97 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.30), residues: 742 helix: 2.47 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.01 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.014 0.002 PHE E 67 TYR 0.012 0.002 TYR F 51 ARG 0.007 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.05299 ( 782) hydrogen bonds : angle 2.92701 ( 1952) covalent geometry : bond 0.00419 (12758) covalent geometry : angle 0.59424 (18479) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.880 Fit side-chains REVERT: A 39 HIS cc_start: 0.5708 (OUTLIER) cc_final: 0.5165 (p-80) REVERT: C 99 ARG cc_start: 0.7841 (mmt180) cc_final: 0.7341 (mmm160) REVERT: E 86 ARG cc_start: 0.7919 (ttt180) cc_final: 0.7697 (tpt170) REVERT: F 79 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8749 (mtmt) REVERT: G 15 LYS cc_start: 0.7995 (mtpm) cc_final: 0.7614 (mtmt) REVERT: G 56 GLU cc_start: 0.8850 (tt0) cc_final: 0.8646 (tt0) REVERT: G 77 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7644 (mtp180) outliers start: 12 outliers final: 6 residues processed: 159 average time/residue: 2.0300 time to fit residues: 338.2624 Evaluate side-chains 159 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.164302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123753 restraints weight = 10080.572| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 0.91 r_work: 0.3235 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 12758 Z= 0.253 Angle : 0.642 9.130 18479 Z= 0.386 Chirality : 0.040 0.175 2104 Planarity : 0.005 0.047 1336 Dihedral : 30.607 73.777 4006 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.39 % Allowed : 14.17 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.30), residues: 742 helix: 2.29 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.04 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 129 PHE 0.014 0.002 PHE E 67 TYR 0.014 0.002 TYR F 51 ARG 0.006 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.06141 ( 782) hydrogen bonds : angle 3.01068 ( 1952) covalent geometry : bond 0.00556 (12758) covalent geometry : angle 0.64176 (18479) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 1.027 Fit side-chains REVERT: C 61 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8102 (tp30) REVERT: C 99 ARG cc_start: 0.7706 (mmt180) cc_final: 0.7108 (mmm160) REVERT: E 59 GLU cc_start: 0.8459 (pm20) cc_final: 0.7918 (pm20) REVERT: E 86 ARG cc_start: 0.7973 (ttt180) cc_final: 0.7662 (tpt170) REVERT: F 79 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8720 (mtmm) REVERT: G 15 LYS cc_start: 0.7998 (mtpm) cc_final: 0.7611 (mtmt) REVERT: G 77 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7654 (mtp180) REVERT: G 95 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8018 (tmtt) REVERT: H 105 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7502 (mm-30) outliers start: 15 outliers final: 7 residues processed: 160 average time/residue: 2.0171 time to fit residues: 338.2945 Evaluate side-chains 162 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 104 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.164957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124466 restraints weight = 10052.671| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 0.90 r_work: 0.3245 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12758 Z= 0.211 Angle : 0.622 8.760 18479 Z= 0.376 Chirality : 0.038 0.169 2104 Planarity : 0.005 0.053 1336 Dihedral : 30.607 73.751 4006 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.39 % Allowed : 14.49 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.30), residues: 742 helix: 2.35 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.06 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.015 0.002 PHE E 67 TYR 0.014 0.002 TYR F 51 ARG 0.006 0.000 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.05756 ( 782) hydrogen bonds : angle 2.98875 ( 1952) covalent geometry : bond 0.00457 (12758) covalent geometry : angle 0.62184 (18479) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.852 Fit side-chains REVERT: A 39 HIS cc_start: 0.5711 (OUTLIER) cc_final: 0.5173 (p-80) REVERT: C 99 ARG cc_start: 0.7726 (mmt180) cc_final: 0.7132 (mmm160) REVERT: E 59 GLU cc_start: 0.8452 (pm20) cc_final: 0.7908 (pm20) REVERT: E 86 ARG cc_start: 0.7925 (ttt180) cc_final: 0.7615 (tpt170) REVERT: F 79 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8715 (mtmt) REVERT: G 15 LYS cc_start: 0.7972 (mtpm) cc_final: 0.7572 (mtmt) REVERT: G 77 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7645 (mtp180) REVERT: H 105 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7510 (mm-30) outliers start: 15 outliers final: 8 residues processed: 159 average time/residue: 2.0292 time to fit residues: 338.1620 Evaluate side-chains 162 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.165702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126003 restraints weight = 10080.123| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 0.94 r_work: 0.3237 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12758 Z= 0.205 Angle : 0.610 8.332 18479 Z= 0.369 Chirality : 0.037 0.166 2104 Planarity : 0.005 0.056 1336 Dihedral : 30.576 73.656 4006 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.23 % Allowed : 14.97 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.30), residues: 742 helix: 2.37 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.02 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.014 0.002 PHE E 67 TYR 0.018 0.002 TYR D 83 ARG 0.012 0.000 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.05541 ( 782) hydrogen bonds : angle 2.95252 ( 1952) covalent geometry : bond 0.00443 (12758) covalent geometry : angle 0.60967 (18479) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.826 Fit side-chains REVERT: A 39 HIS cc_start: 0.5708 (OUTLIER) cc_final: 0.5182 (p-80) REVERT: C 99 ARG cc_start: 0.7772 (mmt180) cc_final: 0.7173 (mmm160) REVERT: E 59 GLU cc_start: 0.8472 (pm20) cc_final: 0.7948 (pm20) REVERT: E 86 ARG cc_start: 0.7969 (ttt180) cc_final: 0.7680 (tpt170) REVERT: F 79 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8745 (mtmt) REVERT: G 15 LYS cc_start: 0.8002 (mtpm) cc_final: 0.7617 (mtmt) REVERT: G 77 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7708 (mtp180) REVERT: G 95 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8075 (tmtt) REVERT: H 105 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7577 (mm-30) outliers start: 14 outliers final: 8 residues processed: 160 average time/residue: 2.0535 time to fit residues: 344.1615 Evaluate side-chains 166 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 52 optimal weight: 0.0970 chunk 81 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 63 ASN D 84 ASN G 24 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.165305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125393 restraints weight = 10074.338| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 0.95 r_work: 0.3224 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 12758 Z= 0.226 Angle : 0.620 8.635 18479 Z= 0.374 Chirality : 0.038 0.166 2104 Planarity : 0.005 0.044 1336 Dihedral : 30.558 73.501 4006 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.39 % Allowed : 14.97 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.30), residues: 742 helix: 2.32 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.01 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 129 PHE 0.014 0.002 PHE E 67 TYR 0.019 0.002 TYR F 88 ARG 0.005 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.05727 ( 782) hydrogen bonds : angle 2.96033 ( 1952) covalent geometry : bond 0.00493 (12758) covalent geometry : angle 0.61959 (18479) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.864 Fit side-chains REVERT: C 99 ARG cc_start: 0.7770 (mmt180) cc_final: 0.7190 (mmm160) REVERT: E 59 GLU cc_start: 0.8475 (pm20) cc_final: 0.7954 (pm20) REVERT: F 79 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8716 (mtmm) REVERT: G 15 LYS cc_start: 0.8008 (mtpm) cc_final: 0.7627 (mtmt) REVERT: G 77 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7711 (mtp180) REVERT: G 95 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8447 (ttmm) outliers start: 15 outliers final: 8 residues processed: 159 average time/residue: 2.0514 time to fit residues: 341.5925 Evaluate side-chains 163 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 0.4980 chunk 84 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 63 ASN D 84 ASN G 24 GLN G 104 GLN H 47 GLN H 82 HIS H 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.166895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.126481 restraints weight = 10033.490| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 0.90 r_work: 0.3270 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12758 Z= 0.165 Angle : 0.595 8.132 18479 Z= 0.361 Chirality : 0.035 0.161 2104 Planarity : 0.005 0.077 1336 Dihedral : 30.543 73.382 4006 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.75 % Allowed : 15.45 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.30), residues: 742 helix: 2.45 (0.21), residues: 554 sheet: None (None), residues: 0 loop : 0.00 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 109 PHE 0.015 0.001 PHE E 67 TYR 0.015 0.002 TYR F 88 ARG 0.011 0.000 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 782) hydrogen bonds : angle 2.94092 ( 1952) covalent geometry : bond 0.00342 (12758) covalent geometry : angle 0.59546 (18479) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.818 Fit side-chains REVERT: C 99 ARG cc_start: 0.7677 (mmt180) cc_final: 0.7080 (mmm160) REVERT: F 79 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8672 (mtmm) REVERT: G 15 LYS cc_start: 0.7968 (mtpm) cc_final: 0.7569 (mtmt) REVERT: G 77 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7655 (mtp180) outliers start: 11 outliers final: 7 residues processed: 157 average time/residue: 2.0609 time to fit residues: 338.9557 Evaluate side-chains 160 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 63 ASN G 24 GLN G 104 GLN H 47 GLN H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.165584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.124858 restraints weight = 10023.474| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 0.90 r_work: 0.3253 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12758 Z= 0.210 Angle : 0.609 8.215 18479 Z= 0.368 Chirality : 0.037 0.163 2104 Planarity : 0.005 0.049 1336 Dihedral : 30.489 73.091 4006 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.91 % Allowed : 15.76 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.30), residues: 742 helix: 2.48 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.12 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.014 0.002 PHE E 67 TYR 0.019 0.002 TYR F 88 ARG 0.007 0.001 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.05479 ( 782) hydrogen bonds : angle 2.92965 ( 1952) covalent geometry : bond 0.00455 (12758) covalent geometry : angle 0.60913 (18479) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12057.74 seconds wall clock time: 207 minutes 0.79 seconds (12420.79 seconds total)