Starting phenix.real_space_refine on Tue Jul 29 19:09:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kb5_37070/07_2025/8kb5_37070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kb5_37070/07_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_37070/07_2025/8kb5_37070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kb5_37070/07_2025/8kb5_37070.map" model { file = "/net/cci-nas-00/data/ceres_data/8kb5_37070/07_2025/8kb5_37070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kb5_37070/07_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.11, per 1000 atoms: 0.59 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: 2.66 Conformation dependent library (CDL) restraints added in 901.5 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: 5.62 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: 4.36 Time building geometry restraints manager: 3.22 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: 0.770 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.010 Find NCS groups from input model: 0.370 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:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.490 ------------------------------------------------------------------------------- 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 : 0.864 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: 2.2745 time to fit residues: 377.4870 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 : 0.842 ------------------------------------------------------------------------------- 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 = 59)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124403 restraints weight = 9964.647| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 0.91 r_work: 0.3241 rms_B_bonded: 1.89 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 : 0.934 Fit side-chains revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8129 (tp30) cc_final: 0.7908 (tp30) REVERT: C 71 ARG cc_start: 0.7198 (ttm110) cc_final: 0.6988 (ttp80) REVERT: C 99 ARG cc_start: 0.7799 (mmt180) cc_final: 0.7326 (mmm160) REVERT: G 15 LYS cc_start: 0.8003 (mtpm) cc_final: 0.7618 (mtmt) outliers start: 9 outliers final: 3 residues processed: 161 average time/residue: 2.0420 time to fit residues: 344.4704 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 : 0.877 ------------------------------------------------------------------------------- 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 84 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.164672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.124904 restraints weight = 10116.232| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 0.93 r_work: 0.3223 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0883 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 8.723 18479 Z= 0.384 Chirality : 0.040 0.172 2104 Planarity : 0.005 0.044 1336 Dihedral : 30.591 74.415 4006 Min Nonbonded Distance : 2.575 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 0.05990 ( 782) hydrogen bonds : angle 3.01903 ( 1952) covalent geometry : bond 0.00523 (12758) covalent geometry : angle 0.63543 (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 : 0.872 Fit side-chains REVERT: C 99 ARG cc_start: 0.7882 (mmt180) cc_final: 0.7387 (mmm160) REVERT: E 59 GLU cc_start: 0.8515 (pm20) cc_final: 0.8009 (pm20) REVERT: F 79 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8765 (mtmt) REVERT: G 15 LYS cc_start: 0.8071 (mtpm) cc_final: 0.7677 (mtmt) REVERT: G 90 ASP cc_start: 0.8395 (t70) cc_final: 0.8183 (t70) outliers start: 13 outliers final: 6 residues processed: 160 average time/residue: 2.1213 time to fit residues: 355.5013 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 : 0.922 ------------------------------------------------------------------------------- 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: 1.9990 chunk 34 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.165140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.125674 restraints weight = 9953.401| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 0.89 r_work: 0.3228 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0930 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= 0.222 Angle : 0.620 8.539 18479 Z= 0.376 Chirality : 0.039 0.168 2104 Planarity : 0.005 0.046 1336 Dihedral : 30.581 74.094 4006 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.23 % Allowed : 14.33 % 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: 2.63 (0.30), residues: 742 helix: 2.33 (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 0.005 0.001 HIS B 75 PHE 0.014 0.002 PHE E 67 TYR 0.017 0.002 TYR H 83 ARG 0.007 0.001 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.05748 ( 782) hydrogen bonds : angle 2.98891 ( 1952) covalent geometry : bond 0.00483 (12758) covalent geometry : angle 0.62024 (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 169 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.824 Fit side-chains REVERT: C 99 ARG cc_start: 0.7879 (mmt180) cc_final: 0.7396 (mmm160) REVERT: E 59 GLU cc_start: 0.8485 (pm20) cc_final: 0.7957 (pm20) REVERT: F 79 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8759 (mtmt) REVERT: G 15 LYS cc_start: 0.8030 (mtpm) cc_final: 0.7659 (mtmt) outliers start: 14 outliers final: 6 residues processed: 158 average time/residue: 2.1038 time to fit residues: 348.2754 Evaluate side-chains 159 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 H residue 112 SER 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: 0.0980 chunk 96 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.166013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126466 restraints weight = 10045.937| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 0.93 r_work: 0.3245 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: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12758 Z= 0.183 Angle : 0.600 8.114 18479 Z= 0.365 Chirality : 0.036 0.163 2104 Planarity : 0.005 0.059 1336 Dihedral : 30.571 74.018 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 : 1.59 % Allowed : 15.45 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.46 (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 0.013 0.002 TYR F 51 ARG 0.007 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.05329 ( 782) hydrogen bonds : angle 2.96337 ( 1952) covalent geometry : bond 0.00389 (12758) covalent geometry : angle 0.59962 (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 165 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.856 Fit side-chains REVERT: A 39 HIS cc_start: 0.5724 (OUTLIER) cc_final: 0.5193 (p-80) REVERT: C 99 ARG cc_start: 0.7854 (mmt180) cc_final: 0.7363 (mmm160) REVERT: E 59 GLU cc_start: 0.8468 (pm20) cc_final: 0.7936 (pm20) REVERT: E 86 ARG cc_start: 0.7879 (ttt180) cc_final: 0.7614 (tpt170) REVERT: F 79 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8743 (mtmt) REVERT: G 15 LYS cc_start: 0.8013 (mtpm) cc_final: 0.7633 (mtmt) outliers start: 10 outliers final: 5 residues processed: 158 average time/residue: 2.0613 time to fit residues: 341.4569 Evaluate side-chains 158 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.163891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123725 restraints weight = 10069.466| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 0.95 r_work: 0.3210 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 12758 Z= 0.286 Angle : 0.673 9.452 18479 Z= 0.402 Chirality : 0.042 0.180 2104 Planarity : 0.006 0.048 1336 Dihedral : 30.708 73.804 4006 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 2.43 (0.29), residues: 742 helix: 2.18 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.08 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 129 PHE 0.015 0.002 PHE E 67 TYR 0.016 0.003 TYR F 51 ARG 0.006 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.06574 ( 782) hydrogen bonds : angle 3.06501 ( 1952) covalent geometry : bond 0.00632 (12758) covalent geometry : angle 0.67284 (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 169 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.876 Fit side-chains REVERT: A 39 HIS cc_start: 0.5784 (OUTLIER) cc_final: 0.5252 (p-80) REVERT: C 99 ARG cc_start: 0.7794 (mmt180) cc_final: 0.7213 (mmm160) REVERT: D 47 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8398 (tt0) REVERT: E 59 GLU cc_start: 0.8527 (pm20) cc_final: 0.7995 (pm20) REVERT: E 86 ARG cc_start: 0.8112 (ttt180) cc_final: 0.7871 (tpt170) REVERT: F 79 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8751 (mtmm) REVERT: G 15 LYS cc_start: 0.8129 (mtpm) cc_final: 0.7713 (mtmt) REVERT: G 77 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7714 (mtp180) REVERT: H 105 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7660 (mm-30) outliers start: 15 outliers final: 7 residues processed: 159 average time/residue: 2.1796 time to fit residues: 362.3656 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 : 0.860 ------------------------------------------------------------------------------- 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 47 GLN 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 46 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: 0.9990 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.165151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124500 restraints weight = 10040.703| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 0.91 r_work: 0.3240 rms_B_bonded: 1.91 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: 0.8254 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12758 Z= 0.205 Angle : 0.624 8.762 18479 Z= 0.378 Chirality : 0.038 0.170 2104 Planarity : 0.005 0.057 1336 Dihedral : 30.699 73.746 4006 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.23 % Allowed : 15.29 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.56 (0.30), residues: 742 helix: 2.29 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.11 (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 0.015 0.002 TYR D 83 ARG 0.015 0.001 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.05801 ( 782) hydrogen bonds : angle 3.00817 ( 1952) covalent geometry : bond 0.00440 (12758) covalent geometry : angle 0.62442 (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 168 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 1.553 Fit side-chains REVERT: A 39 HIS cc_start: 0.5757 (OUTLIER) cc_final: 0.5219 (p-80) REVERT: C 99 ARG cc_start: 0.7738 (mmt180) cc_final: 0.7150 (mmm160) REVERT: E 59 GLU cc_start: 0.8501 (pm20) cc_final: 0.7987 (pm20) REVERT: E 86 ARG cc_start: 0.8011 (ttt180) cc_final: 0.7765 (tpt170) REVERT: F 79 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8715 (mtmm) REVERT: G 15 LYS cc_start: 0.8005 (mtpm) cc_final: 0.7614 (mtmt) REVERT: G 77 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7651 (mtp180) REVERT: H 105 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7573 (mm-30) outliers start: 14 outliers final: 7 residues processed: 158 average time/residue: 2.9551 time to fit residues: 489.8549 Evaluate side-chains 162 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.166143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.126356 restraints weight = 10093.564| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 0.94 r_work: 0.3236 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12758 Z= 0.187 Angle : 0.605 7.960 18479 Z= 0.366 Chirality : 0.037 0.165 2104 Planarity : 0.006 0.103 1336 Dihedral : 30.637 73.584 4006 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.07 % Allowed : 15.45 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.70 (0.30), residues: 742 helix: 2.40 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.05 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.013 0.002 PHE E 67 TYR 0.030 0.002 TYR H 83 ARG 0.011 0.000 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.05351 ( 782) hydrogen bonds : angle 2.94667 ( 1952) covalent geometry : bond 0.00397 (12758) covalent geometry : angle 0.60460 (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 168 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.926 Fit side-chains REVERT: A 39 HIS cc_start: 0.5728 (OUTLIER) cc_final: 0.5200 (p-80) REVERT: C 99 ARG cc_start: 0.7766 (mmt180) cc_final: 0.7182 (mmm160) REVERT: E 59 GLU cc_start: 0.8470 (pm20) cc_final: 0.7941 (pm20) REVERT: E 86 ARG cc_start: 0.8033 (ttt180) cc_final: 0.7778 (tpt170) REVERT: F 79 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8740 (mtmt) REVERT: G 15 LYS cc_start: 0.8001 (mtpm) cc_final: 0.7619 (mtmt) REVERT: G 77 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7682 (mtp180) REVERT: H 105 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7643 (mm-30) outliers start: 13 outliers final: 7 residues processed: 160 average time/residue: 2.2729 time to fit residues: 381.2443 Evaluate side-chains 164 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 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: 2.9990 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: 0.9980 chunk 81 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 E 125 GLN G 24 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 = 0.164367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123342 restraints weight = 10063.363| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 0.92 r_work: 0.3231 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 12758 Z= 0.256 Angle : 0.648 9.075 18479 Z= 0.388 Chirality : 0.040 0.171 2104 Planarity : 0.005 0.052 1336 Dihedral : 30.669 73.475 4006 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.91 % Allowed : 15.61 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.50 (0.29), residues: 742 helix: 2.24 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.07 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 129 PHE 0.015 0.002 PHE E 67 TYR 0.019 0.003 TYR H 83 ARG 0.006 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.06165 ( 782) hydrogen bonds : angle 3.01189 ( 1952) covalent geometry : bond 0.00563 (12758) covalent geometry : angle 0.64759 (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 166 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.860 Fit side-chains REVERT: A 39 HIS cc_start: 0.5797 (OUTLIER) cc_final: 0.5288 (p-80) REVERT: C 99 ARG cc_start: 0.7717 (mmt180) cc_final: 0.7124 (mmm160) REVERT: E 59 GLU cc_start: 0.8466 (pm20) cc_final: 0.7917 (pm20) REVERT: E 86 ARG cc_start: 0.8046 (ttt180) cc_final: 0.7788 (tpt170) REVERT: F 79 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8676 (mtmm) REVERT: G 15 LYS cc_start: 0.8010 (mtpm) cc_final: 0.7594 (mtmt) REVERT: G 77 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7657 (mtp180) REVERT: H 105 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7581 (mm-30) outliers start: 12 outliers final: 7 residues processed: 158 average time/residue: 2.1612 time to fit residues: 357.2833 Evaluate side-chains 163 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 40 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 E 125 GLN G 24 GLN G 104 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 = 0.165002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124599 restraints weight = 9997.274| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 0.90 r_work: 0.3246 rms_B_bonded: 1.87 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: 0.8227 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12758 Z= 0.205 Angle : 0.631 11.550 18479 Z= 0.379 Chirality : 0.038 0.169 2104 Planarity : 0.005 0.054 1336 Dihedral : 30.670 73.472 4006 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.91 % Allowed : 15.92 % Favored : 82.17 % 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: 2.57 (0.30), residues: 742 helix: 2.30 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.07 (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 0.025 0.002 TYR H 83 ARG 0.006 0.000 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.05776 ( 782) hydrogen bonds : angle 2.99021 ( 1952) covalent geometry : bond 0.00442 (12758) covalent geometry : angle 0.63116 (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 166 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.987 Fit side-chains REVERT: A 39 HIS cc_start: 0.5796 (OUTLIER) cc_final: 0.5283 (p-80) REVERT: C 99 ARG cc_start: 0.7705 (mmt180) cc_final: 0.7112 (mmm160) REVERT: E 59 GLU cc_start: 0.8459 (pm20) cc_final: 0.7910 (pm20) REVERT: E 86 ARG cc_start: 0.8008 (ttt180) cc_final: 0.7751 (tpt170) REVERT: F 79 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8667 (mtmm) REVERT: G 15 LYS cc_start: 0.7984 (mtpm) cc_final: 0.7583 (mtmt) REVERT: G 77 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7642 (mtp180) REVERT: H 105 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7548 (mm-30) outliers start: 12 outliers final: 7 residues processed: 158 average time/residue: 2.1437 time to fit residues: 354.6496 Evaluate side-chains 162 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 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 59 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 E 125 GLN 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 = 0.3988 r_free = 0.3988 target = 0.165807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.125512 restraints weight = 10031.806| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 0.90 r_work: 0.3258 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12758 Z= 0.184 Angle : 0.611 8.110 18479 Z= 0.369 Chirality : 0.036 0.165 2104 Planarity : 0.005 0.046 1336 Dihedral : 30.641 73.367 4006 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.23 % Allowed : 15.61 % Favored : 82.17 % 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: 2.71 (0.30), residues: 742 helix: 2.40 (0.21), residues: 554 sheet: None (None), residues: 0 loop : -0.04 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 129 PHE 0.013 0.002 PHE E 67 TYR 0.027 0.002 TYR H 83 ARG 0.012 0.000 ARG H 79 Details of bonding type rmsd hydrogen bonds : bond 0.05376 ( 782) hydrogen bonds : angle 2.95291 ( 1952) covalent geometry : bond 0.00389 (12758) covalent geometry : angle 0.61138 (18479) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12884.94 seconds wall clock time: 222 minutes 17.40 seconds (13337.40 seconds total)