Starting phenix.real_space_refine on Fri Oct 23 05:00:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zhy_11221/10_2026/6zhy_11221.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zhy_11221/10_2026/6zhy_11221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zhy_11221/10_2026/6zhy_11221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zhy_11221/10_2026/6zhy_11221.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zhy_11221/10_2026/6zhy_11221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zhy_11221/10_2026/6zhy_11221.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 218 5.49 5 S 8 5.16 5 C 4968 2.51 5 N 1700 2.21 5 O 2105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8999 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 813 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" 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: "F" 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: "I" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2236 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Chain: "J" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2268 Classifications: {'DNA': 110} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 109} Chain: "K" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Time building chain proxies: 1.50, per 1000 atoms: 0.17 Number of scatterers: 8999 At special positions: 0 Unit cell: (115.758, 107.256, 101.37, 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 8 16.00 P 218 15.00 O 2105 8.00 N 1700 7.00 C 4968 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: 0.79 Conformation dependent library (CDL) restraints added in 175.8 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 73.5% alpha, 2.5% beta 110 base pairs and 196 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.097A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.860A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (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 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.787A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) 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: 4.400A 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 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.588A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.818A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.663A 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 'C' and resid 42 through 43 removed outlier: 7.157A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.620A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.472A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 306 hydrogen bonds defined for protein. 894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 285 hydrogen bonds 570 hydrogen bond angles 0 basepair planarities 110 basepair parallelities 196 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 0.98 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: 1561 1.33 - 1.45: 3291 1.45 - 1.57: 4300 1.57 - 1.69: 437 1.69 - 1.81: 16 Bond restraints: 9605 Sorted by residual: bond pdb=" C3' DC I 6 " pdb=" C2' DC I 6 " ideal model delta sigma weight residual 1.516 1.562 -0.046 8.00e-03 1.56e+04 3.31e+01 bond pdb=" C3' DT J 69 " pdb=" C2' DT J 69 " ideal model delta sigma weight residual 1.516 1.561 -0.045 8.00e-03 1.56e+04 3.20e+01 bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.516 1.561 -0.045 8.00e-03 1.56e+04 3.18e+01 bond pdb=" C3' DG J -19 " pdb=" C2' DG J -19 " ideal model delta sigma weight residual 1.516 1.557 -0.041 8.00e-03 1.56e+04 2.68e+01 bond pdb=" C3' DT I 15 " pdb=" C2' DT I 15 " ideal model delta sigma weight residual 1.516 1.556 -0.040 8.00e-03 1.56e+04 2.55e+01 ... (remaining 9600 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 12583 1.62 - 3.24: 1008 3.24 - 4.86: 272 4.86 - 6.48: 41 6.48 - 8.10: 3 Bond angle restraints: 13907 Sorted by residual: angle pdb=" O4' DG I -19 " pdb=" C1' DG I -19 " pdb=" N9 DG I -19 " ideal model delta sigma weight residual 108.00 113.63 -5.63 7.00e-01 2.04e+00 6.46e+01 angle pdb=" O4' DG I 26 " pdb=" C1' DG I 26 " pdb=" N9 DG I 26 " ideal model delta sigma weight residual 108.00 102.78 5.22 7.00e-01 2.04e+00 5.57e+01 angle pdb=" O4' DG I 28 " pdb=" C1' DG I 28 " pdb=" N9 DG I 28 " ideal model delta sigma weight residual 108.00 102.99 5.01 7.00e-01 2.04e+00 5.13e+01 angle pdb=" O4' DG J -36 " pdb=" C1' DG J -36 " pdb=" N9 DG J -36 " ideal model delta sigma weight residual 108.00 112.85 -4.85 7.00e-01 2.04e+00 4.79e+01 angle pdb=" O4' DA I -35 " pdb=" C1' DA I -35 " pdb=" N9 DA I -35 " ideal model delta sigma weight residual 108.00 103.32 4.68 7.00e-01 2.04e+00 4.47e+01 ... (remaining 13902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.42: 4197 33.42 - 66.83: 967 66.83 - 100.25: 36 100.25 - 133.66: 0 133.66 - 167.07: 2 Dihedral angle restraints: 5202 sinusoidal: 3573 harmonic: 1629 Sorted by residual: dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual 180.00 153.18 26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA THR D 85 " pdb=" C THR D 85 " pdb=" N ILE D 86 " pdb=" CA ILE D 86 " ideal model delta harmonic sigma weight residual 180.00 157.65 22.35 0 5.00e+00 4.00e-02 2.00e+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 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 5199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1221 0.072 - 0.144: 298 0.144 - 0.216: 41 0.216 - 0.287: 13 0.287 - 0.359: 6 Chirality restraints: 1579 Sorted by residual: chirality pdb=" C3' DG J 20 " pdb=" C4' DG J 20 " pdb=" O3' DG J 20 " pdb=" C2' DG J 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.37 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" C4' DT J 69 " pdb=" C5' DT J 69 " pdb=" O4' DT J 69 " pdb=" C3' DT J 69 " both_signs ideal model delta sigma weight residual False -2.53 -2.18 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.39 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 1576 not shown) Planarity restraints: 999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 6 " -0.063 2.00e-02 2.50e+03 3.45e-02 2.67e+01 pdb=" N1 DC I 6 " 0.075 2.00e-02 2.50e+03 pdb=" C2 DC I 6 " -0.016 2.00e-02 2.50e+03 pdb=" O2 DC I 6 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DC I 6 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 6 " -0.007 2.00e-02 2.50e+03 pdb=" N4 DC I 6 " -0.020 2.00e-02 2.50e+03 pdb=" C5 DC I 6 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DC I 6 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 4 " -0.053 2.00e-02 2.50e+03 3.09e-02 2.14e+01 pdb=" N1 DC I 4 " 0.071 2.00e-02 2.50e+03 pdb=" C2 DC I 4 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DC I 4 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DC I 4 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 4 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 4 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DC I 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC I 4 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 19 " -0.042 2.00e-02 2.50e+03 2.86e-02 1.84e+01 pdb=" N1 DC J 19 " 0.069 2.00e-02 2.50e+03 pdb=" C2 DC J 19 " -0.025 2.00e-02 2.50e+03 pdb=" O2 DC J 19 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC J 19 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC J 19 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC J 19 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC J 19 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC J 19 " 0.002 2.00e-02 2.50e+03 ... (remaining 996 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2053 2.83 - 3.35: 8482 3.35 - 3.87: 18066 3.87 - 4.38: 21277 4.38 - 4.90: 29320 Nonbonded interactions: 79198 Sorted by model distance: nonbonded pdb=" OE1 GLN B 93 " pdb=" NH1 ARG B 95 " model vdw 2.316 3.120 nonbonded pdb=" NH2 ARG E 116 " pdb=" OD1 ASP E 123 " model vdw 2.376 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.406 3.040 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.420 3.040 nonbonded pdb=" OE1 GLU D 68 " pdb=" NZ LYS F 91 " model vdw 2.427 3.120 ... (remaining 79193 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' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 102) selection = chain 'F' } 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: 0.960 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.120 Find NCS groups from input model: 0.080 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 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 0.082 9605 Z= 0.661 Angle : 1.014 8.099 13907 Z= 0.885 Chirality : 0.069 0.359 1579 Planarity : 0.014 0.138 999 Dihedral : 27.253 167.075 4150 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.21 % Allowed : 0.43 % Favored : 99.36 % 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: 0.65 (0.31), residues: 548 helix: 0.73 (0.23), residues: 394 sheet: None (None), residues: 0 loop : -0.05 (0.44), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.004 ARG A 83 TYR 0.027 0.004 TYR C 57 PHE 0.010 0.001 PHE F 100 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.66 ( 9605) covalent geometry : angle 1.01391 / 0.89 (13907) hydrogen bonds : bond 0.12610 / 8.39 ( 591) hydrogen bonds : angle 4.54469 / 3.38 ( 1464) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: B 74 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7738 (mt-10) REVERT: C 90 ASP cc_start: 0.8348 (t70) cc_final: 0.8132 (t70) REVERT: F 31 LYS cc_start: 0.8916 (tttt) cc_final: 0.8649 (tttp) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.7584 time to fit residues: 144.2540 Evaluate side-chains 124 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 27] chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 68 GLN A 125 GLN C 73 ASN D 92 GLN E 68 GLN E 85 GLN E 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.081122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.055740 restraints weight = 24140.552| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.12 r_work: 0.2750 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9605 Z= 0.172 Angle : 0.805 9.103 13907 Z= 0.460 Chirality : 0.057 0.257 1579 Planarity : 0.006 0.057 999 Dihedral : 31.916 164.879 3019 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 4.48 % Allowed : 15.57 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.32 (0.34), residues: 548 helix: 2.11 (0.25), residues: 399 sheet: None (None), residues: 0 loop : 0.02 (0.46), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 83 TYR 0.013 0.001 TYR C 57 PHE 0.007 0.001 PHE F 100 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.17 ( 9605) covalent geometry : angle 0.80511 / 0.46 (13907) hydrogen bonds : bond 0.05669 / 3.74 ( 591) hydrogen bonds : angle 3.25109 / 2.44 ( 1464) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8798 (mmp-170) REVERT: C 90 ASP cc_start: 0.8437 (t70) cc_final: 0.8220 (t70) REVERT: E 59 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8204 (pm20) REVERT: F 31 LYS cc_start: 0.8999 (tttt) cc_final: 0.8772 (tttp) REVERT: F 79 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.9012 (ttmm) outliers start: 21 outliers final: 11 residues processed: 148 average time/residue: 0.6598 time to fit residues: 102.8495 Evaluate side-chains 139 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [55, 28, 35, 16, 61, 57, 11, 45, 53, 69, 39] chunk 55 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN E 68 GLN E 108 ASN E 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.080416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.055139 restraints weight = 23992.496| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.08 r_work: 0.2735 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9605 Z= 0.167 Angle : 0.726 7.788 13907 Z= 0.422 Chirality : 0.053 0.300 1579 Planarity : 0.006 0.067 999 Dihedral : 32.117 164.878 3019 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.48 % Allowed : 18.98 % Favored : 76.55 % 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: 3.01 (0.36), residues: 548 helix: 2.55 (0.26), residues: 402 sheet: None (None), residues: 0 loop : 0.43 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 83 TYR 0.011 0.001 TYR C 57 PHE 0.020 0.002 PHE E 78 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.17 ( 9605) covalent geometry : angle 0.72610 / 0.42 (13907) hydrogen bonds : bond 0.05052 / 3.29 ( 591) hydrogen bonds : angle 3.04490 / 2.27 ( 1464) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8742 (mmp-170) REVERT: B 35 ARG cc_start: 0.9306 (mmm-85) cc_final: 0.9071 (mmm-85) REVERT: C 56 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: E 120 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8593 (mtm) outliers start: 21 outliers final: 6 residues processed: 141 average time/residue: 0.6533 time to fit residues: 97.0341 Evaluate side-chains 133 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [19, 52, 62, 15, 26, 2, 65, 14, 13, 4, 30] chunk 19 optimal weight: 0.5980 chunk 52 optimal weight: 30.0000 chunk 62 optimal weight: 40.0000 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 68 ASN D 44 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.081407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.056147 restraints weight = 24445.934| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.13 r_work: 0.2767 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9605 Z= 0.142 Angle : 0.690 7.913 13907 Z= 0.402 Chirality : 0.050 0.298 1579 Planarity : 0.005 0.040 999 Dihedral : 31.999 167.495 3019 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.26 % Allowed : 20.68 % Favored : 75.05 % 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: 3.26 (0.36), residues: 548 helix: 2.74 (0.26), residues: 402 sheet: None (None), residues: 0 loop : 0.54 (0.51), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.008 0.001 TYR C 57 PHE 0.013 0.001 PHE E 78 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.14 ( 9605) covalent geometry : angle 0.69029 / 0.40 (13907) hydrogen bonds : bond 0.04293 / 2.82 ( 591) hydrogen bonds : angle 2.84280 / 2.13 ( 1464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8667 (mttm) REVERT: A 90 MET cc_start: 0.8721 (mmm) cc_final: 0.8414 (mmm) REVERT: B 35 ARG cc_start: 0.9322 (mmm-85) cc_final: 0.9100 (mmm-85) REVERT: C 56 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8498 (tt0) REVERT: C 92 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8602 (mt-10) REVERT: E 120 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8447 (mtm) outliers start: 20 outliers final: 12 residues processed: 138 average time/residue: 0.6498 time to fit residues: 94.3953 Evaluate side-chains 139 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [41, 67, 64, 52, 42, 72, 30, 39, 14, 12, 29] chunk 41 optimal weight: 0.9980 chunk 67 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 52 optimal weight: 30.0000 chunk 42 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 113 HIS E 68 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.081333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.056253 restraints weight = 24389.918| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.11 r_work: 0.2775 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9605 Z= 0.142 Angle : 0.667 7.272 13907 Z= 0.389 Chirality : 0.048 0.318 1579 Planarity : 0.005 0.046 999 Dihedral : 31.915 170.037 3019 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.84 % Allowed : 22.17 % Favored : 73.99 % 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: 3.34 (0.35), residues: 548 helix: 2.79 (0.25), residues: 403 sheet: None (None), residues: 0 loop : 0.55 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.007 0.001 TYR C 57 PHE 0.009 0.001 PHE F 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 ( 9605) covalent geometry : angle 0.66734 / 0.39 (13907) hydrogen bonds : bond 0.04260 / 2.79 ( 591) hydrogen bonds : angle 2.77989 / 2.08 ( 1464) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8496 (tt0) outliers start: 18 outliers final: 8 residues processed: 136 average time/residue: 0.6846 time to fit residues: 97.9688 Evaluate side-chains 132 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [54, 41, 50, 43, 11, 5, 46, 6, 32, 16, 25] chunk 54 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 39 HIS E 68 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.080453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.055114 restraints weight = 24297.321| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.11 r_work: 0.2743 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9605 Z= 0.167 Angle : 0.681 7.238 13907 Z= 0.389 Chirality : 0.047 0.342 1579 Planarity : 0.005 0.046 999 Dihedral : 31.925 174.243 3019 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 4.48 % Allowed : 22.81 % Favored : 72.71 % 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: 3.27 (0.36), residues: 548 helix: 2.77 (0.25), residues: 403 sheet: None (None), residues: 0 loop : 0.44 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 35 TYR 0.010 0.001 TYR D 80 PHE 0.015 0.001 PHE E 78 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.17 ( 9605) covalent geometry : angle 0.68084 / 0.39 (13907) hydrogen bonds : bond 0.04399 / 2.87 ( 591) hydrogen bonds : angle 2.85968 / 2.15 ( 1464) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8496 (tt0) outliers start: 21 outliers final: 8 residues processed: 137 average time/residue: 0.6607 time to fit residues: 95.4320 Evaluate side-chains 134 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [17, 37, 20, 44, 65, 57, 13, 70, 66, 25, 43] chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.080340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.055329 restraints weight = 24474.772| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.08 r_work: 0.2744 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9605 Z= 0.165 Angle : 0.676 7.312 13907 Z= 0.386 Chirality : 0.046 0.358 1579 Planarity : 0.005 0.050 999 Dihedral : 31.836 179.071 3019 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.84 % Allowed : 23.67 % Favored : 72.49 % 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: 3.16 (0.36), residues: 548 helix: 2.73 (0.25), residues: 405 sheet: None (None), residues: 0 loop : 0.23 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 35 TYR 0.007 0.001 TYR C 57 PHE 0.016 0.001 PHE E 78 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 ( 9605) covalent geometry : angle 0.67601 / 0.39 (13907) hydrogen bonds : bond 0.04257 / 2.77 ( 591) hydrogen bonds : angle 2.83529 / 2.13 ( 1464) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8520 (tt0) REVERT: D 90 GLU cc_start: 0.8532 (mp0) cc_final: 0.8067 (mp0) outliers start: 18 outliers final: 9 residues processed: 137 average time/residue: 0.6824 time to fit residues: 98.1812 Evaluate side-chains 133 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [36, 43, 7, 49, 25, 53, 63, 40, 38, 70, 29] chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 63 optimal weight: 50.0000 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.080555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.055392 restraints weight = 24237.612| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.11 r_work: 0.2745 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9605 Z= 0.153 Angle : 0.666 8.769 13907 Z= 0.382 Chirality : 0.045 0.363 1579 Planarity : 0.005 0.046 999 Dihedral : 31.737 177.895 3019 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.35 % Allowed : 25.80 % Favored : 71.86 % 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: 3.24 (0.36), residues: 548 helix: 2.80 (0.25), residues: 405 sheet: None (None), residues: 0 loop : 0.20 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 35 TYR 0.010 0.001 TYR F 88 PHE 0.012 0.001 PHE E 78 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 ( 9605) covalent geometry : angle 0.66646 / 0.38 (13907) hydrogen bonds : bond 0.04112 / 2.68 ( 591) hydrogen bonds : angle 2.82411 / 2.12 ( 1464) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: E 59 GLU cc_start: 0.8712 (pm20) cc_final: 0.8144 (pm20) outliers start: 11 outliers final: 6 residues processed: 136 average time/residue: 0.6560 time to fit residues: 93.7211 Evaluate side-chains 132 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 80 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [25, 47, 63, 1, 72, 36, 15, 26, 17, 13, 50] chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 50.0000 chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.079413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.053838 restraints weight = 24187.000| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.08 r_work: 0.2708 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9605 Z= 0.201 Angle : 0.697 8.187 13907 Z= 0.390 Chirality : 0.046 0.376 1579 Planarity : 0.005 0.048 999 Dihedral : 31.817 173.886 3019 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.56 % Allowed : 25.16 % Favored : 72.28 % 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: 3.14 (0.36), residues: 548 helix: 2.72 (0.25), residues: 403 sheet: None (None), residues: 0 loop : 0.22 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 35 TYR 0.011 0.002 TYR F 88 PHE 0.011 0.002 PHE E 78 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 ( 9605) covalent geometry : angle 0.69691 / 0.39 (13907) hydrogen bonds : bond 0.04704 / 3.07 ( 591) hydrogen bonds : angle 2.93506 / 2.20 ( 1464) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8541 (tt0) REVERT: D 90 GLU cc_start: 0.8523 (mp0) cc_final: 0.8065 (mp0) REVERT: E 59 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8229 (pm20) outliers start: 12 outliers final: 6 residues processed: 129 average time/residue: 0.6920 time to fit residues: 93.9332 Evaluate side-chains 126 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [68, 54, 25, 9, 13, 4, 52, 30, 67, 42, 21] chunk 68 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 30.0000 chunk 30 optimal weight: 0.7980 chunk 67 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.080314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.055073 restraints weight = 24104.839| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.09 r_work: 0.2739 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9605 Z= 0.144 Angle : 0.669 8.780 13907 Z= 0.380 Chirality : 0.045 0.368 1579 Planarity : 0.005 0.047 999 Dihedral : 31.743 172.403 3019 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.13 % Allowed : 24.95 % Favored : 72.92 % 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: 3.23 (0.36), residues: 548 helix: 2.79 (0.25), residues: 402 sheet: None (None), residues: 0 loop : 0.24 (0.52), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 35 TYR 0.016 0.001 TYR F 88 PHE 0.013 0.001 PHE E 78 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 ( 9605) covalent geometry : angle 0.66885 / 0.38 (13907) hydrogen bonds : bond 0.04067 / 2.66 ( 591) hydrogen bonds : angle 2.84304 / 2.13 ( 1464) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8520 (tt0) REVERT: D 90 GLU cc_start: 0.8504 (mp0) cc_final: 0.8030 (mp0) REVERT: E 59 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8263 (pm20) outliers start: 10 outliers final: 4 residues processed: 135 average time/residue: 0.6898 time to fit residues: 97.8012 Evaluate side-chains 130 residues out of total 469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: [10, 19, 39, 70, 14, 55, 58, 41, 63, 57, 29] chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 14 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 63 optimal weight: 50.0000 chunk 57 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.079399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.054102 restraints weight = 23802.475| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.06 r_work: 0.2714 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9605 Z= 0.192 Angle : 0.686 8.829 13907 Z= 0.384 Chirality : 0.045 0.372 1579 Planarity : 0.005 0.046 999 Dihedral : 31.727 167.975 3019 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.35 % Allowed : 24.31 % Favored : 73.35 % 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: 3.21 (0.36), residues: 548 helix: 2.77 (0.25), residues: 403 sheet: None (None), residues: 0 loop : 0.24 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 35 TYR 0.013 0.002 TYR D 80 PHE 0.011 0.002 PHE E 78 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 ( 9605) covalent geometry : angle 0.68554 / 0.38 (13907) hydrogen bonds : bond 0.04558 / 2.98 ( 591) hydrogen bonds : angle 2.94190 / 2.20 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2985.53 seconds wall clock time: 51 minutes 20.43 seconds (3080.43 seconds total)