Starting phenix.real_space_refine on Fri Sep 11 18:57:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nl0_12453/09_2026/7nl0_12453.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nl0_12453/09_2026/7nl0_12453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nl0_12453/09_2026/7nl0_12453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nl0_12453/09_2026/7nl0_12453.map" model { file = "/net/cci-nas-00/data/ceres_data/7nl0_12453/09_2026/7nl0_12453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nl0_12453/09_2026/7nl0_12453.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 262 5.49 5 S 14 5.16 5 C 6334 2.51 5 N 2121 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11363 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2715 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "J" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2656 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Time building chain proxies: 2.48, per 1000 atoms: 0.22 Number of scatterers: 11363 At special positions: 0 Unit cell: (75.9676, 120.12, 116.873, 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 14 16.00 P 262 15.00 O 2632 8.00 N 2121 7.00 C 6334 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: 0.88 Conformation dependent library (CDL) restraints added in 170.4 milliseconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 73.0% alpha, 2.4% beta 127 base pairs and 223 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.820A 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 24 through 29 removed outlier: 3.671A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.802A 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: 4.505A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.591A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.500A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.787A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.638A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.727A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.513A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.350A 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: 7.413A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.676A 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: 7.283A 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 77 through 78 409 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 307 hydrogen bonds 614 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 223 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.13 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: 2176 1.33 - 1.45: 3809 1.45 - 1.57: 5564 1.57 - 1.69: 522 1.69 - 1.81: 24 Bond restraints: 12095 Sorted by residual: bond pdb=" C3' DT J 51 " pdb=" C2' DT J 51 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.49e+01 bond pdb=" C3' DA J 34 " pdb=" C2' DA J 34 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.43e+01 bond pdb=" C3' DT I 60 " pdb=" C2' DT I 60 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.39e+01 bond pdb=" C3' DT J 8 " pdb=" O3' DT J 8 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.37e+01 bond pdb=" C3' DA I 58 " pdb=" O3' DA I 58 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.26e+01 ... (remaining 12090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 16045 1.61 - 3.21: 1305 3.21 - 4.82: 84 4.82 - 6.43: 16 6.43 - 8.04: 1 Bond angle restraints: 17451 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.71 107.75 5.96 9.50e-01 1.11e+00 3.94e+01 angle pdb=" O4' DG I 57 " pdb=" C4' DG I 57 " pdb=" C3' DG I 57 " ideal model delta sigma weight residual 106.00 102.74 3.26 6.00e-01 2.78e+00 2.95e+01 angle pdb=" O4' DG I 47 " pdb=" C4' DG I 47 " pdb=" C3' DG I 47 " ideal model delta sigma weight residual 106.00 103.00 3.00 6.00e-01 2.78e+00 2.50e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.89 -2.99 6.00e-01 2.78e+00 2.48e+01 angle pdb=" N3 DT I 70 " pdb=" C4 DT I 70 " pdb=" O4 DT I 70 " ideal model delta sigma weight residual 119.90 122.70 -2.80 6.00e-01 2.78e+00 2.18e+01 ... (remaining 17446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 5243 35.14 - 70.28: 1400 70.28 - 105.43: 23 105.43 - 140.57: 3 140.57 - 175.71: 9 Dihedral angle restraints: 6678 sinusoidal: 4495 harmonic: 2183 Sorted by residual: dihedral pdb=" CA TYR G 39 " pdb=" C TYR G 39 " pdb=" N SER G 40 " pdb=" CA SER G 40 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" C4' DG J 30 " pdb=" C3' DG J 30 " pdb=" O3' DG J 30 " pdb=" P DA J 31 " ideal model delta sinusoidal sigma weight residual -140.00 35.71 -175.71 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " pdb=" P DG I -16 " ideal model delta sinusoidal sigma weight residual -140.00 33.83 -173.83 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1179 0.036 - 0.073: 589 0.073 - 0.109: 161 0.109 - 0.145: 46 0.145 - 0.182: 8 Chirality restraints: 1983 Sorted by residual: chirality pdb=" C3' DA I 58 " pdb=" C4' DA I 58 " pdb=" O3' DA I 58 " pdb=" C2' DA I 58 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" C3' DA I 14 " pdb=" C4' DA I 14 " pdb=" O3' DA I 14 " pdb=" C2' DA I 14 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" C3' DC J 57 " pdb=" C4' DC J 57 " pdb=" O3' DC J 57 " pdb=" C2' DC J 57 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 1980 not shown) Planarity restraints: 1305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -24 " -0.027 2.00e-02 2.50e+03 1.18e-02 3.80e+00 pdb=" N9 DA I -24 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA I -24 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I -24 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DA I -24 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -24 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I -24 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -24 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -24 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I -24 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -24 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 16 " 0.027 2.00e-02 2.50e+03 1.10e-02 3.66e+00 pdb=" N9 DG I 16 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DG I 16 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 16 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DG I 16 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DG I 16 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG I 16 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DG I 16 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG I 16 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG I 16 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 16 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 16 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " 0.025 2.00e-02 2.50e+03 1.08e-02 3.50e+00 pdb=" N9 DG I 28 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " -0.002 2.00e-02 2.50e+03 ... (remaining 1302 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 559 2.70 - 3.25: 9965 3.25 - 3.80: 22342 3.80 - 4.35: 27582 4.35 - 4.90: 39438 Nonbonded interactions: 99886 Sorted by model distance: nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.147 3.040 nonbonded pdb=" OD1 ASP C 90 " pdb=" N GLU C 91 " model vdw 2.185 3.120 nonbonded pdb=" NE ARG A 131 " pdb=" OE2 GLU A 133 " model vdw 2.233 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.237 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.251 3.120 ... (remaining 99881 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' and (resid 39 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 13 through 117) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.620 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.160 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 0.067 12095 Z= 0.585 Angle : 0.866 8.036 17451 Z= 0.762 Chirality : 0.046 0.182 1983 Planarity : 0.004 0.040 1305 Dihedral : 29.742 175.712 5272 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.30), residues: 739 helix: 1.29 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -1.90 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 32 TYR 0.012 0.002 TYR F 51 PHE 0.024 0.003 PHE C 25 HIS 0.007 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.59 (12095) covalent geometry : angle 0.86616 / 0.76 (17451) hydrogen bonds : bond 0.11327 / 7.77 ( 716) hydrogen bonds : angle 4.81605 / 3.53 ( 1826) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.312 Fit side-chains REVERT: E 59 GLU cc_start: 0.7178 (pp20) cc_final: 0.6896 (pm20) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1534 time to fit residues: 26.4633 Evaluate side-chains 121 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 92 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.141720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.104001 restraints weight = 18481.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.106124 restraints weight = 12482.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.107464 restraints weight = 10059.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108126 restraints weight = 8997.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.108561 restraints weight = 8507.393| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12095 Z= 0.161 Angle : 0.740 8.697 17451 Z= 0.416 Chirality : 0.051 0.374 1983 Planarity : 0.005 0.040 1305 Dihedral : 32.935 172.752 3777 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.28 % Allowed : 7.66 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.31), residues: 739 helix: 1.69 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.77 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 128 TYR 0.016 0.002 TYR C 57 PHE 0.015 0.002 PHE C 25 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (12095) covalent geometry : angle 0.73953 / 0.42 (17451) hydrogen bonds : bond 0.05813 / 3.89 ( 716) hydrogen bonds : angle 3.51449 / 2.61 ( 1826) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.328 Fit side-chains REVERT: E 59 GLU cc_start: 0.7265 (pp20) cc_final: 0.7019 (pm20) outliers start: 8 outliers final: 7 residues processed: 134 average time/residue: 0.1538 time to fit residues: 26.7765 Evaluate side-chains 131 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 63 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.141240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.102445 restraints weight = 18600.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.104822 restraints weight = 11951.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.106332 restraints weight = 9352.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107052 restraints weight = 8265.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107053 restraints weight = 7773.050| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12095 Z= 0.182 Angle : 0.708 7.834 17451 Z= 0.404 Chirality : 0.050 0.385 1983 Planarity : 0.004 0.037 1305 Dihedral : 32.931 176.267 3777 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.59 % Allowed : 10.85 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.31), residues: 739 helix: 1.92 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.79 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.010 0.002 TYR F 51 PHE 0.014 0.002 PHE A 67 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 (12095) covalent geometry : angle 0.70832 / 0.40 (17451) hydrogen bonds : bond 0.05671 / 3.77 ( 716) hydrogen bonds : angle 3.36959 / 2.50 ( 1826) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.305 Fit side-chains REVERT: E 59 GLU cc_start: 0.7276 (pp20) cc_final: 0.7054 (pm20) outliers start: 10 outliers final: 9 residues processed: 128 average time/residue: 0.1468 time to fit residues: 24.8716 Evaluate side-chains 131 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 94 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN E 125 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.139364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.099946 restraints weight = 18750.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.102356 restraints weight = 11883.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.103860 restraints weight = 9307.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.104674 restraints weight = 8200.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.105028 restraints weight = 7694.335| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 12095 Z= 0.235 Angle : 0.743 8.264 17451 Z= 0.415 Chirality : 0.051 0.392 1983 Planarity : 0.005 0.037 1305 Dihedral : 33.013 176.507 3777 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.71 % Allowed : 11.64 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.31), residues: 739 helix: 1.84 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.84 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 29 TYR 0.012 0.002 TYR C 50 PHE 0.016 0.003 PHE G 25 HIS 0.008 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 (12095) covalent geometry : angle 0.74318 / 0.41 (17451) hydrogen bonds : bond 0.05988 / 3.97 ( 716) hydrogen bonds : angle 3.37166 / 2.50 ( 1826) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.223 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 130 average time/residue: 0.1522 time to fit residues: 25.7878 Evaluate side-chains 133 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 86 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 50 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.141164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.102877 restraints weight = 18642.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.104999 restraints weight = 12543.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106316 restraints weight = 10114.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.107008 restraints weight = 9095.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.107008 restraints weight = 8619.690| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12095 Z= 0.175 Angle : 0.697 7.969 17451 Z= 0.394 Chirality : 0.049 0.378 1983 Planarity : 0.004 0.040 1305 Dihedral : 32.972 177.623 3777 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.39 % Allowed : 12.76 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.30), residues: 739 helix: 2.04 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.83 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 83 TYR 0.022 0.002 TYR C 39 PHE 0.013 0.002 PHE A 67 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (12095) covalent geometry : angle 0.69737 / 0.39 (17451) hydrogen bonds : bond 0.05186 / 3.44 ( 716) hydrogen bonds : angle 3.23078 / 2.39 ( 1826) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.287 Fit side-chains REVERT: B 77 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8654 (mmtt) outliers start: 15 outliers final: 14 residues processed: 130 average time/residue: 0.1322 time to fit residues: 23.0291 Evaluate side-chains 134 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.0370 chunk 60 optimal weight: 0.9980 chunk 62 optimal weight: 0.2980 chunk 82 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.143462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.105454 restraints weight = 18752.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107631 restraints weight = 12495.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.109024 restraints weight = 10048.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109788 restraints weight = 8940.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.109891 restraints weight = 8448.573| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12095 Z= 0.137 Angle : 0.653 7.621 17451 Z= 0.375 Chirality : 0.047 0.375 1983 Planarity : 0.004 0.043 1305 Dihedral : 32.825 179.624 3777 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.44 % Allowed : 14.83 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.31), residues: 739 helix: 2.30 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.56 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 42 TYR 0.011 0.001 TYR C 39 PHE 0.014 0.002 PHE A 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.14 (12095) covalent geometry : angle 0.65320 / 0.37 (17451) hydrogen bonds : bond 0.04520 / 3.01 ( 716) hydrogen bonds : angle 3.04713 / 2.27 ( 1826) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.302 Fit side-chains REVERT: H 69 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.8230 (mtm180) REVERT: H 86 ILE cc_start: 0.8945 (mp) cc_final: 0.8726 (mp) REVERT: H 90 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7308 (mt-10) outliers start: 9 outliers final: 5 residues processed: 140 average time/residue: 0.1464 time to fit residues: 26.8887 Evaluate side-chains 131 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 51 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 44 optimal weight: 0.0770 chunk 40 optimal weight: 0.6980 chunk 75 optimal weight: 20.0000 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.143121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.104299 restraints weight = 18671.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.106926 restraints weight = 11484.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108506 restraints weight = 8824.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.109425 restraints weight = 7728.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.109514 restraints weight = 7228.652| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12095 Z= 0.138 Angle : 0.649 7.823 17451 Z= 0.371 Chirality : 0.047 0.379 1983 Planarity : 0.004 0.042 1305 Dihedral : 32.790 179.630 3777 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.23 % Allowed : 14.19 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.31), residues: 739 helix: 2.49 (0.21), residues: 546 sheet: None (None), residues: 0 loop : -1.50 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.010 0.001 TYR C 57 PHE 0.014 0.002 PHE A 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (12095) covalent geometry : angle 0.64886 / 0.37 (17451) hydrogen bonds : bond 0.04529 / 3.04 ( 716) hydrogen bonds : angle 2.99931 / 2.23 ( 1826) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.324 Fit side-chains REVERT: B 79 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7728 (mtmm) REVERT: H 69 ARG cc_start: 0.8470 (mtm-85) cc_final: 0.8203 (mtm180) REVERT: H 86 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8717 (mp) REVERT: H 90 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7356 (mt-10) outliers start: 14 outliers final: 8 residues processed: 132 average time/residue: 0.1390 time to fit residues: 24.3906 Evaluate side-chains 136 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 57 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.143641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105628 restraints weight = 18684.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.107792 restraints weight = 12480.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.109039 restraints weight = 10070.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109822 restraints weight = 9039.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.109906 restraints weight = 8543.429| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12095 Z= 0.137 Angle : 0.645 7.751 17451 Z= 0.368 Chirality : 0.046 0.378 1983 Planarity : 0.004 0.043 1305 Dihedral : 32.771 179.135 3777 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.07 % Allowed : 14.99 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.31), residues: 739 helix: 2.53 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -1.36 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 83 TYR 0.011 0.001 TYR C 57 PHE 0.014 0.002 PHE A 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.14 (12095) covalent geometry : angle 0.64506 / 0.37 (17451) hydrogen bonds : bond 0.04422 / 2.96 ( 716) hydrogen bonds : angle 2.97345 / 2.21 ( 1826) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.289 Fit side-chains REVERT: B 79 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7681 (mtmm) REVERT: E 56 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7477 (mtmt) REVERT: H 69 ARG cc_start: 0.8478 (mtm-85) cc_final: 0.8245 (mtm180) REVERT: H 90 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7377 (mt-10) outliers start: 13 outliers final: 7 residues processed: 132 average time/residue: 0.1498 time to fit residues: 26.1518 Evaluate side-chains 136 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 72 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 52 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.144169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.105738 restraints weight = 18486.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108186 restraints weight = 11747.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.109735 restraints weight = 9214.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110600 restraints weight = 8102.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110771 restraints weight = 7608.350| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12095 Z= 0.130 Angle : 0.637 7.663 17451 Z= 0.366 Chirality : 0.046 0.373 1983 Planarity : 0.004 0.044 1305 Dihedral : 32.737 178.604 3777 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.59 % Allowed : 15.15 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.31), residues: 739 helix: 2.57 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -1.31 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 83 TYR 0.009 0.001 TYR H 37 PHE 0.014 0.002 PHE A 67 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.13 (12095) covalent geometry : angle 0.63703 / 0.37 (17451) hydrogen bonds : bond 0.04300 / 2.88 ( 716) hydrogen bonds : angle 2.92820 / 2.18 ( 1826) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.315 Fit side-chains REVERT: B 79 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7666 (mtmm) REVERT: E 56 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7424 (mtmt) REVERT: H 69 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.8271 (mtm180) REVERT: H 90 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7344 (mt-10) outliers start: 10 outliers final: 7 residues processed: 134 average time/residue: 0.1361 time to fit residues: 24.1578 Evaluate side-chains 137 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 25 optimal weight: 0.0670 chunk 41 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.144372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.106313 restraints weight = 18778.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.108470 restraints weight = 12496.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109836 restraints weight = 10072.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.110588 restraints weight = 8992.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.110595 restraints weight = 8490.996| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12095 Z= 0.135 Angle : 0.636 7.719 17451 Z= 0.364 Chirality : 0.046 0.375 1983 Planarity : 0.004 0.043 1305 Dihedral : 32.701 177.853 3777 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.75 % Allowed : 15.31 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.31), residues: 739 helix: 2.62 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -1.03 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.009 0.001 TYR H 37 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (12095) covalent geometry : angle 0.63611 / 0.36 (17451) hydrogen bonds : bond 0.04340 / 2.91 ( 716) hydrogen bonds : angle 2.94675 / 2.19 ( 1826) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.324 Fit side-chains REVERT: B 79 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7672 (mtmm) REVERT: C 38 ASN cc_start: 0.6911 (OUTLIER) cc_final: 0.6591 (t0) REVERT: E 56 LYS cc_start: 0.7767 (mtmt) cc_final: 0.7487 (mtmt) REVERT: H 69 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.8278 (mtm180) REVERT: H 90 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7362 (mt-10) outliers start: 11 outliers final: 5 residues processed: 136 average time/residue: 0.1473 time to fit residues: 26.5152 Evaluate side-chains 136 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 90 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.143026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.104659 restraints weight = 18733.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.106786 restraints weight = 12623.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.107920 restraints weight = 10194.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.108799 restraints weight = 9179.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.108820 restraints weight = 8666.137| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12095 Z= 0.166 Angle : 0.659 7.913 17451 Z= 0.372 Chirality : 0.047 0.380 1983 Planarity : 0.004 0.043 1305 Dihedral : 32.741 178.175 3777 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.44 % Allowed : 15.79 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.31), residues: 739 helix: 2.52 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -1.09 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.009 0.001 TYR C 50 PHE 0.011 0.002 PHE A 67 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (12095) covalent geometry : angle 0.65905 / 0.37 (17451) hydrogen bonds : bond 0.04730 / 3.17 ( 716) hydrogen bonds : angle 3.00535 / 2.23 ( 1826) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1707.46 seconds wall clock time: 30 minutes 14.55 seconds (1814.55 seconds total)