Starting phenix.real_space_refine on Thu Jul 2 11:46:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5w_33627/07_2026/7y5w_33627.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5w_33627/07_2026/7y5w_33627.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 { model { file = "/net/cci-nas-00/data/ceres_data/7y5w_33627/07_2026/7y5w_33627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5w_33627/07_2026/7y5w_33627.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y5w_33627/07_2026/7y5w_33627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5w_33627/07_2026/7y5w_33627.map" } 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= 0.017 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 202 5.49 5 S 20 5.16 5 C 4911 2.51 5 N 1652 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8811 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 561 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "C" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 608 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "D" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "E" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 615 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "G" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 591 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "H" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 524 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "I" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2054 Classifications: {'DNA': 101} Link IDs: {'rna3p': 100} Chain: "J" Number of atoms: 2087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2087 Classifications: {'DNA': 101} Link IDs: {'rna3p': 100} Time building chain proxies: 1.53, per 1000 atoms: 0.17 Number of scatterers: 8811 At special positions: 0 Unit cell: (82, 114, 116, 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 20 16.00 P 202 15.00 O 2026 8.00 N 1652 7.00 C 4911 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: 0.73 Conformation dependent library (CDL) restraints added in 293.4 milliseconds 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1100 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 5 sheets defined 79.1% alpha, 1.7% beta 90 base pairs and 167 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.505A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.653A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.501A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 47 through 76 removed outlier: 4.209A pdb=" N TYR D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU D 52 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'E' and resid 63 through 79 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: 3.503A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.548A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.561A pdb=" N PHE G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 132 removed outlier: 3.803A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 77 Processing helix chain 'H' and resid 82 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 84 removed outlier: 7.247A pdb=" N ARG C 83 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.326A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 349 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 231 hydrogen bonds 442 hydrogen bond angles 0 basepair planarities 90 basepair parallelities 167 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1879 1.34 - 1.45: 2816 1.45 - 1.57: 4233 1.57 - 1.69: 402 1.69 - 1.81: 32 Bond restraints: 9362 Sorted by residual: bond pdb=" C3' DA I 103 " pdb=" C2' DA I 103 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DG I 85 " pdb=" C2' DG I 85 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.80e+00 bond pdb=" C3' DC I 64 " pdb=" C2' DC I 64 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.32e+00 bond pdb=" C3' DG I 63 " pdb=" C2' DG I 63 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.22e+00 bond pdb=" C3' DG I 76 " pdb=" C2' DG I 76 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.21e+00 ... (remaining 9357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 12925 1.80 - 3.61: 539 3.61 - 5.41: 23 5.41 - 7.22: 0 7.22 - 9.02: 1 Bond angle restraints: 13488 Sorted by residual: angle pdb=" O4' DG I 121 " pdb=" C4' DG I 121 " pdb=" C3' DG I 121 " ideal model delta sigma weight residual 106.00 103.04 2.96 6.00e-01 2.78e+00 2.43e+01 angle pdb=" O4' DG I 101 " pdb=" C4' DG I 101 " pdb=" C3' DG I 101 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT I 104 " pdb=" C4 DT I 104 " pdb=" O4 DT I 104 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 angle pdb=" O4' DA I 60 " pdb=" C4' DA I 60 " pdb=" C3' DA I 60 " ideal model delta sigma weight residual 106.00 103.37 2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" O4' DT I 105 " pdb=" C1' DT I 105 " pdb=" N1 DT I 105 " ideal model delta sigma weight residual 108.00 111.06 -3.06 7.00e-01 2.04e+00 1.91e+01 ... (remaining 13483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.06: 3940 29.06 - 58.13: 1086 58.13 - 87.19: 104 87.19 - 116.25: 1 116.25 - 145.31: 4 Dihedral angle restraints: 5135 sinusoidal: 3448 harmonic: 1687 Sorted by residual: dihedral pdb=" C4' DG I 73 " pdb=" C3' DG I 73 " pdb=" O3' DG I 73 " pdb=" P DC I 74 " ideal model delta sinusoidal sigma weight residual 220.00 74.69 145.31 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" C4' DT J 105 " pdb=" C3' DT J 105 " pdb=" O3' DT J 105 " pdb=" P DG J 106 " ideal model delta sinusoidal sigma weight residual 220.00 89.58 130.42 1 3.50e+01 8.16e-04 1.29e+01 dihedral pdb=" C4' DG I 34 " pdb=" C3' DG I 34 " pdb=" O3' DG I 34 " pdb=" P DT I 35 " ideal model delta sinusoidal sigma weight residual 220.00 91.20 128.80 1 3.50e+01 8.16e-04 1.27e+01 ... (remaining 5132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 837 0.029 - 0.059: 464 0.059 - 0.088: 168 0.088 - 0.118: 72 0.118 - 0.147: 8 Chirality restraints: 1549 Sorted by residual: chirality pdb=" C3' DG I 73 " pdb=" C4' DG I 73 " pdb=" O3' DG I 73 " pdb=" C2' DG I 73 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA ILE D 29 " pdb=" N ILE D 29 " pdb=" C ILE D 29 " pdb=" CB ILE D 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" C3' DA J 40 " pdb=" C4' DA J 40 " pdb=" O3' DA J 40 " pdb=" C2' DA J 40 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 1546 not shown) Planarity restraints: 1004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET G 120 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO G 121 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO G 121 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 121 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 121 " -0.023 2.00e-02 2.50e+03 1.04e-02 3.24e+00 pdb=" N9 DG I 121 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 121 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 121 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 121 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 121 " -0.001 2.00e-02 2.50e+03 pdb=" O6 DG I 121 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 121 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 121 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG I 121 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 121 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 110 " -0.020 2.00e-02 2.50e+03 9.51e-03 2.04e+00 pdb=" N1 DC I 110 " 0.016 2.00e-02 2.50e+03 pdb=" C2 DC I 110 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 110 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DC I 110 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC I 110 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 110 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 110 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 110 " 0.004 2.00e-02 2.50e+03 ... (remaining 1001 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 219 2.66 - 3.22: 7704 3.22 - 3.78: 17065 3.78 - 4.34: 20536 4.34 - 4.90: 29648 Nonbonded interactions: 75172 Sorted by model distance: nonbonded pdb=" N2 DG I 34 " pdb=" O2 DC J 114 " model vdw 2.102 2.496 nonbonded pdb=" N2 DG I 33 " pdb=" O2 DC J 115 " model vdw 2.118 2.496 nonbonded pdb=" N2 DG I 85 " pdb=" O2 DC J 63 " model vdw 2.139 2.496 nonbonded pdb=" O2 DC I 82 " pdb=" N2 DG J 66 " model vdw 2.156 2.496 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.228 3.040 ... (remaining 75167 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 61 through 133) selection = (chain 'C' and resid 61 through 133) selection = (chain 'E' and resid 61 through 133) selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 29 through 93) selection = (chain 'D' and resid 29 through 93) selection = (chain 'F' and resid 29 through 93) 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: 1.190 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: 8.800 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 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 : 0.005 0.040 9362 Z= 0.491 Angle : 0.705 9.023 13488 Z= 0.631 Chirality : 0.043 0.147 1549 Planarity : 0.003 0.045 1004 Dihedral : 27.557 145.314 4035 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.34), residues: 563 helix: 2.20 (0.23), residues: 458 sheet: None (None), residues: 0 loop : -0.72 (0.50), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 129 TYR 0.008 0.001 TYR B 51 PHE 0.007 0.001 PHE E 67 HIS 0.003 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.49 ( 9362) covalent geometry : angle 0.70479 / 0.63 (13488) hydrogen bonds : bond 0.09757 / 6.46 ( 580) hydrogen bonds : angle 3.60096 / 2.58 ( 1477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 ASP cc_start: 0.6597 (t70) cc_final: 0.6280 (t0) REVERT: E 60 LEU cc_start: 0.7307 (mt) cc_final: 0.6991 (mt) REVERT: F 80 THR cc_start: 0.8225 (m) cc_final: 0.7965 (p) REVERT: G 89 VAL cc_start: 0.8828 (m) cc_final: 0.8532 (m) REVERT: G 90 MET cc_start: 0.7212 (tmm) cc_final: 0.6304 (tmm) REVERT: H 60 VAL cc_start: 0.8165 (t) cc_final: 0.7948 (p) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.1342 time to fit residues: 54.3404 Evaluate side-chains 224 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 overall best weight: 3.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 93 GLN C 68 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.057736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.041202 restraints weight = 55214.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.042510 restraints weight = 26880.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.043351 restraints weight = 17784.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.043748 restraints weight = 13981.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.044123 restraints weight = 12416.658| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 9362 Z= 0.283 Angle : 0.803 14.337 13488 Z= 0.451 Chirality : 0.047 0.250 1549 Planarity : 0.007 0.067 1004 Dihedral : 30.906 145.352 2840 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.87 % Allowed : 27.94 % Favored : 66.19 % 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: 1.75 (0.34), residues: 563 helix: 1.63 (0.23), residues: 463 sheet: None (None), residues: 0 loop : -1.01 (0.54), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 67 TYR 0.018 0.002 TYR H 88 PHE 0.020 0.003 PHE C 78 HIS 0.008 0.002 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.28 ( 9362) covalent geometry : angle 0.80273 / 0.45 (13488) hydrogen bonds : bond 0.07153 / 4.73 ( 580) hydrogen bonds : angle 3.71809 / 2.72 ( 1477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 250 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8898 (tp30) cc_final: 0.8682 (tp30) REVERT: A 120 MET cc_start: 0.8626 (mtm) cc_final: 0.8399 (mtm) REVERT: A 134 ARG cc_start: 0.8777 (tpp-160) cc_final: 0.8272 (tpp-160) REVERT: B 63 GLU cc_start: 0.9342 (mt-10) cc_final: 0.9008 (mm-30) REVERT: B 68 ASP cc_start: 0.8739 (t70) cc_final: 0.8405 (t0) REVERT: B 92 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8225 (ttp80) REVERT: C 60 LEU cc_start: 0.8977 (mm) cc_final: 0.8410 (mm) REVERT: C 73 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8585 (tm-30) REVERT: C 77 ASP cc_start: 0.8968 (t70) cc_final: 0.8664 (t0) REVERT: C 97 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7995 (mt-10) REVERT: E 85 GLN cc_start: 0.9385 (OUTLIER) cc_final: 0.9167 (tt0) REVERT: E 120 MET cc_start: 0.8085 (mmm) cc_final: 0.7856 (mmm) REVERT: E 129 ARG cc_start: 0.8792 (mmm160) cc_final: 0.8231 (mmm160) REVERT: F 44 LYS cc_start: 0.9549 (OUTLIER) cc_final: 0.9239 (mmmt) REVERT: F 79 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8450 (mtmm) REVERT: F 80 THR cc_start: 0.9359 (m) cc_final: 0.8900 (p) REVERT: F 88 TYR cc_start: 0.9043 (m-80) cc_final: 0.8835 (m-10) REVERT: G 90 MET cc_start: 0.9185 (tmm) cc_final: 0.8809 (tmm) REVERT: G 120 MET cc_start: 0.8457 (mmm) cc_final: 0.8179 (mmm) REVERT: G 131 ARG cc_start: 0.8775 (mtp85) cc_final: 0.8492 (mtp85) REVERT: H 49 LEU cc_start: 0.8075 (mp) cc_final: 0.7812 (mm) REVERT: H 53 GLU cc_start: 0.9333 (mt-10) cc_final: 0.9086 (mt-10) REVERT: H 72 TYR cc_start: 0.9220 (t80) cc_final: 0.9018 (t80) outliers start: 29 outliers final: 20 residues processed: 259 average time/residue: 0.1102 time to fit residues: 36.8140 Evaluate side-chains 247 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 59 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.0970 chunk 70 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 55 optimal weight: 30.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** H 64 ASN ** 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 = 0.3605 r_free = 0.3605 target = 0.058998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.042365 restraints weight = 54118.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.043684 restraints weight = 26664.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.044491 restraints weight = 17882.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.044934 restraints weight = 14224.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.045222 restraints weight = 12565.776| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9362 Z= 0.177 Angle : 0.709 9.215 13488 Z= 0.408 Chirality : 0.044 0.312 1549 Planarity : 0.005 0.046 1004 Dihedral : 31.031 146.867 2840 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.26 % Allowed : 27.73 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.33), residues: 563 helix: 1.41 (0.23), residues: 464 sheet: None (None), residues: 0 loop : -1.04 (0.51), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 36 TYR 0.017 0.002 TYR E 99 PHE 0.024 0.002 PHE A 78 HIS 0.005 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.18 ( 9362) covalent geometry : angle 0.70903 / 0.41 (13488) hydrogen bonds : bond 0.06134 / 4.02 ( 580) hydrogen bonds : angle 3.49751 / 2.57 ( 1477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 260 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8757 (tmm) cc_final: 0.8406 (tmm) REVERT: A 105 GLU cc_start: 0.8874 (tp30) cc_final: 0.8560 (tp30) REVERT: A 112 ILE cc_start: 0.9700 (tp) cc_final: 0.9397 (pt) REVERT: A 120 MET cc_start: 0.8659 (mtm) cc_final: 0.8335 (mtm) REVERT: B 63 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8969 (mm-30) REVERT: B 67 ARG cc_start: 0.9070 (ttm-80) cc_final: 0.8866 (ttm-80) REVERT: B 68 ASP cc_start: 0.8688 (t70) cc_final: 0.8337 (t0) REVERT: B 77 LYS cc_start: 0.8307 (mttp) cc_final: 0.8033 (mmtm) REVERT: C 60 LEU cc_start: 0.8901 (mm) cc_final: 0.8179 (mm) REVERT: C 73 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8653 (tm-30) REVERT: C 77 ASP cc_start: 0.8998 (t70) cc_final: 0.8681 (t0) REVERT: C 97 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7932 (mt-10) REVERT: C 105 GLU cc_start: 0.9021 (tp30) cc_final: 0.8658 (mm-30) REVERT: C 128 ARG cc_start: 0.9463 (mtp85) cc_final: 0.9203 (mtp85) REVERT: C 129 ARG cc_start: 0.9258 (tpp80) cc_final: 0.8871 (tpp80) REVERT: D 79 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8468 (mmmm) REVERT: E 129 ARG cc_start: 0.8838 (mmm160) cc_final: 0.8246 (mmm160) REVERT: F 25 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8510 (t0) REVERT: F 31 LYS cc_start: 0.9326 (ttpp) cc_final: 0.8962 (ttmm) REVERT: F 44 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9204 (mmmt) REVERT: F 79 LYS cc_start: 0.8985 (mtpp) cc_final: 0.8474 (mtmm) REVERT: F 80 THR cc_start: 0.9360 (m) cc_final: 0.8847 (p) REVERT: F 88 TYR cc_start: 0.9045 (m-80) cc_final: 0.8753 (m-10) REVERT: G 90 MET cc_start: 0.9312 (tmm) cc_final: 0.8972 (tpp) REVERT: G 120 MET cc_start: 0.8585 (mmm) cc_final: 0.8321 (mmm) REVERT: G 131 ARG cc_start: 0.8894 (mtp85) cc_final: 0.8562 (mtp85) REVERT: H 47 SER cc_start: 0.7822 (t) cc_final: 0.7461 (t) REVERT: H 49 LEU cc_start: 0.8017 (mp) cc_final: 0.7728 (mm) REVERT: H 53 GLU cc_start: 0.9364 (mt-10) cc_final: 0.9119 (mt-10) outliers start: 26 outliers final: 18 residues processed: 265 average time/residue: 0.1145 time to fit residues: 39.0042 Evaluate side-chains 264 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 244 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 59 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 55 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 61 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 9 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.057676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.041419 restraints weight = 55183.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.042754 restraints weight = 25693.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.043610 restraints weight = 16722.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.044146 restraints weight = 13032.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.044414 restraints weight = 11283.309| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9362 Z= 0.190 Angle : 0.719 9.754 13488 Z= 0.413 Chirality : 0.044 0.285 1549 Planarity : 0.005 0.044 1004 Dihedral : 31.085 147.520 2840 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.26 % Allowed : 30.36 % Favored : 64.37 % 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: 1.41 (0.33), residues: 563 helix: 1.42 (0.23), residues: 463 sheet: None (None), residues: 0 loop : -1.22 (0.48), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 129 TYR 0.018 0.002 TYR E 99 PHE 0.021 0.002 PHE A 78 HIS 0.005 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.19 ( 9362) covalent geometry : angle 0.71865 / 0.41 (13488) hydrogen bonds : bond 0.06198 / 4.09 ( 580) hydrogen bonds : angle 3.54445 / 2.59 ( 1477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 253 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8756 (tmm) cc_final: 0.8292 (tmm) REVERT: A 105 GLU cc_start: 0.8914 (tp30) cc_final: 0.8669 (tm-30) REVERT: A 112 ILE cc_start: 0.9699 (tp) cc_final: 0.9388 (pt) REVERT: A 120 MET cc_start: 0.8601 (mtm) cc_final: 0.8227 (mtm) REVERT: A 128 ARG cc_start: 0.9112 (mtp180) cc_final: 0.8014 (mtp-110) REVERT: A 134 ARG cc_start: 0.8817 (tpp-160) cc_final: 0.8029 (tpp-160) REVERT: B 44 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8667 (mmmm) REVERT: B 53 GLU cc_start: 0.9376 (tp30) cc_final: 0.8994 (tp30) REVERT: B 63 GLU cc_start: 0.9322 (mt-10) cc_final: 0.9070 (mm-30) REVERT: B 68 ASP cc_start: 0.8553 (t70) cc_final: 0.8276 (t0) REVERT: B 77 LYS cc_start: 0.8321 (mttp) cc_final: 0.8054 (mmtm) REVERT: C 73 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8539 (tm-30) REVERT: C 77 ASP cc_start: 0.8998 (t70) cc_final: 0.8728 (t0) REVERT: C 129 ARG cc_start: 0.9282 (tpp80) cc_final: 0.8991 (tpp80) REVERT: D 79 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8497 (mmmm) REVERT: E 115 LYS cc_start: 0.9632 (mmmm) cc_final: 0.9355 (mmmm) REVERT: E 120 MET cc_start: 0.8382 (mmm) cc_final: 0.7972 (mmm) REVERT: E 129 ARG cc_start: 0.8863 (mmm160) cc_final: 0.8244 (mmm160) REVERT: F 23 ARG cc_start: 0.7992 (ptm160) cc_final: 0.7439 (ptm-80) REVERT: F 31 LYS cc_start: 0.9322 (ttpp) cc_final: 0.8964 (ttmm) REVERT: F 44 LYS cc_start: 0.9506 (OUTLIER) cc_final: 0.9219 (mmmm) REVERT: F 52 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8211 (tm-30) REVERT: F 79 LYS cc_start: 0.9003 (mtpp) cc_final: 0.8502 (mtmm) REVERT: F 80 THR cc_start: 0.9380 (m) cc_final: 0.8794 (p) REVERT: F 88 TYR cc_start: 0.9038 (m-80) cc_final: 0.8748 (m-10) REVERT: G 90 MET cc_start: 0.9273 (tmm) cc_final: 0.8888 (tpp) REVERT: G 94 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8965 (pm20) REVERT: G 120 MET cc_start: 0.8540 (mmm) cc_final: 0.8317 (mmm) REVERT: G 131 ARG cc_start: 0.8918 (mtp85) cc_final: 0.8566 (mtp85) REVERT: H 47 SER cc_start: 0.7753 (t) cc_final: 0.7157 (t) REVERT: H 49 LEU cc_start: 0.8082 (mp) cc_final: 0.7876 (mm) REVERT: H 53 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9071 (mt-10) outliers start: 26 outliers final: 20 residues processed: 259 average time/residue: 0.0987 time to fit residues: 33.2679 Evaluate side-chains 262 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 59 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 30.0000 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 64 optimal weight: 30.0000 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** 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 = 0.3580 r_free = 0.3580 target = 0.058360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.041975 restraints weight = 53932.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.043295 restraints weight = 25919.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.044086 restraints weight = 17156.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.044638 restraints weight = 13599.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.044886 restraints weight = 11830.027| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9362 Z= 0.174 Angle : 0.720 10.175 13488 Z= 0.413 Chirality : 0.044 0.299 1549 Planarity : 0.005 0.047 1004 Dihedral : 31.096 148.536 2840 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.67 % Allowed : 30.36 % Favored : 63.97 % 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 (0.33), residues: 563 helix: 1.41 (0.23), residues: 461 sheet: None (None), residues: 0 loop : -1.26 (0.47), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 67 TYR 0.022 0.002 TYR H 72 PHE 0.023 0.002 PHE A 78 HIS 0.004 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 ( 9362) covalent geometry : angle 0.71958 / 0.41 (13488) hydrogen bonds : bond 0.06028 / 3.97 ( 580) hydrogen bonds : angle 3.54284 / 2.61 ( 1477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8764 (tmm) cc_final: 0.8227 (tmm) REVERT: A 105 GLU cc_start: 0.8876 (tp30) cc_final: 0.8631 (tm-30) REVERT: A 112 ILE cc_start: 0.9703 (tp) cc_final: 0.9396 (pt) REVERT: A 120 MET cc_start: 0.8594 (mtm) cc_final: 0.8224 (mtm) REVERT: B 44 LYS cc_start: 0.9000 (mmmt) cc_final: 0.8570 (mmmm) REVERT: B 53 GLU cc_start: 0.9357 (tp30) cc_final: 0.9039 (tp30) REVERT: B 63 GLU cc_start: 0.9325 (mt-10) cc_final: 0.9076 (mm-30) REVERT: B 68 ASP cc_start: 0.8593 (t70) cc_final: 0.8179 (t0) REVERT: C 73 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8514 (tm-30) REVERT: C 77 ASP cc_start: 0.9002 (t70) cc_final: 0.8714 (t0) REVERT: C 85 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.8942 (mt0) REVERT: C 105 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8779 (mm-30) REVERT: C 125 GLN cc_start: 0.9213 (mt0) cc_final: 0.8916 (mp10) REVERT: C 129 ARG cc_start: 0.9233 (tpp80) cc_final: 0.8991 (tpp80) REVERT: D 53 GLU cc_start: 0.9142 (tp30) cc_final: 0.8787 (tp30) REVERT: D 79 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8506 (mmmm) REVERT: E 79 LYS cc_start: 0.8190 (tptt) cc_final: 0.7983 (tptt) REVERT: E 94 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8741 (mm-30) REVERT: E 115 LYS cc_start: 0.9628 (mmmm) cc_final: 0.9382 (mmmm) REVERT: E 129 ARG cc_start: 0.8916 (mmm160) cc_final: 0.8362 (mmm160) REVERT: F 31 LYS cc_start: 0.9330 (ttpp) cc_final: 0.9099 (ttmm) REVERT: F 44 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9190 (mmmm) REVERT: F 52 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8159 (tm-30) REVERT: F 74 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8763 (mm-30) REVERT: F 79 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8538 (mtmm) REVERT: F 80 THR cc_start: 0.9398 (m) cc_final: 0.8806 (p) REVERT: F 88 TYR cc_start: 0.9039 (m-80) cc_final: 0.8788 (m-10) REVERT: G 70 LEU cc_start: 0.9227 (mt) cc_final: 0.8989 (mt) REVERT: G 90 MET cc_start: 0.9282 (tmm) cc_final: 0.8896 (tpp) REVERT: G 131 ARG cc_start: 0.8952 (mtp85) cc_final: 0.8585 (mtp85) REVERT: H 43 VAL cc_start: 0.8173 (t) cc_final: 0.7696 (t) REVERT: H 46 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7594 (tp) REVERT: H 47 SER cc_start: 0.7662 (t) cc_final: 0.6325 (t) REVERT: H 49 LEU cc_start: 0.8111 (mp) cc_final: 0.7892 (mm) REVERT: H 53 GLU cc_start: 0.9361 (mt-10) cc_final: 0.9085 (mt-10) outliers start: 28 outliers final: 17 residues processed: 259 average time/residue: 0.1169 time to fit residues: 38.4058 Evaluate side-chains 253 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 59 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 34 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 chunk 0 optimal weight: 0.9980 chunk 70 optimal weight: 20.0000 chunk 21 optimal weight: 0.0050 chunk 13 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** 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 = 0.3569 r_free = 0.3569 target = 0.057646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.041452 restraints weight = 55601.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.042781 restraints weight = 26871.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.043692 restraints weight = 17762.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.044215 restraints weight = 13767.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.044439 restraints weight = 11902.138| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9362 Z= 0.178 Angle : 0.751 11.591 13488 Z= 0.424 Chirality : 0.044 0.300 1549 Planarity : 0.005 0.054 1004 Dihedral : 31.088 149.139 2840 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.45 % Allowed : 34.21 % Favored : 61.34 % 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: 1.08 (0.33), residues: 563 helix: 1.22 (0.23), residues: 463 sheet: None (None), residues: 0 loop : -1.46 (0.46), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 92 TYR 0.021 0.002 TYR H 72 PHE 0.014 0.002 PHE G 78 HIS 0.003 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.18 ( 9362) covalent geometry : angle 0.75095 / 0.42 (13488) hydrogen bonds : bond 0.05958 / 3.93 ( 580) hydrogen bonds : angle 3.58158 / 2.64 ( 1477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8223 (mm) REVERT: A 90 MET cc_start: 0.8733 (tmm) cc_final: 0.8240 (tmm) REVERT: A 94 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8011 (tm-30) REVERT: A 105 GLU cc_start: 0.8912 (tp30) cc_final: 0.8660 (tm-30) REVERT: A 112 ILE cc_start: 0.9713 (tp) cc_final: 0.9411 (pt) REVERT: A 120 MET cc_start: 0.8667 (mtm) cc_final: 0.8189 (mtm) REVERT: B 44 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8666 (mmmm) REVERT: B 53 GLU cc_start: 0.9408 (tp30) cc_final: 0.8984 (tp30) REVERT: B 68 ASP cc_start: 0.8341 (t70) cc_final: 0.8111 (t0) REVERT: B 91 LYS cc_start: 0.9425 (mmmm) cc_final: 0.9194 (mmmm) REVERT: B 92 ARG cc_start: 0.8711 (ptm-80) cc_final: 0.8335 (ttp80) REVERT: C 73 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8514 (tm-30) REVERT: C 77 ASP cc_start: 0.9019 (t70) cc_final: 0.8739 (t0) REVERT: C 85 GLN cc_start: 0.9366 (mt0) cc_final: 0.8274 (mt0) REVERT: C 105 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8680 (mm-30) REVERT: C 125 GLN cc_start: 0.9253 (mt0) cc_final: 0.8928 (mp10) REVERT: C 129 ARG cc_start: 0.9254 (tpp80) cc_final: 0.8809 (ttp80) REVERT: D 53 GLU cc_start: 0.9201 (tp30) cc_final: 0.8830 (tp30) REVERT: D 79 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8506 (mmmm) REVERT: E 73 GLU cc_start: 0.8862 (tt0) cc_final: 0.8636 (tm-30) REVERT: E 76 GLN cc_start: 0.9276 (pt0) cc_final: 0.8867 (pp30) REVERT: E 115 LYS cc_start: 0.9622 (mmmm) cc_final: 0.9373 (mmmm) REVERT: E 120 MET cc_start: 0.8717 (mmm) cc_final: 0.8084 (mmm) REVERT: E 129 ARG cc_start: 0.8920 (mmm160) cc_final: 0.8385 (mmm160) REVERT: F 31 LYS cc_start: 0.9315 (ttpp) cc_final: 0.9091 (ttmm) REVERT: F 44 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9204 (mmmm) REVERT: F 52 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8180 (tm-30) REVERT: F 79 LYS cc_start: 0.9026 (mtpp) cc_final: 0.8524 (mtmm) REVERT: F 80 THR cc_start: 0.9359 (m) cc_final: 0.8716 (p) REVERT: F 88 TYR cc_start: 0.8984 (m-80) cc_final: 0.8647 (m-10) REVERT: G 70 LEU cc_start: 0.9325 (mt) cc_final: 0.9105 (mt) REVERT: G 93 GLN cc_start: 0.8167 (pt0) cc_final: 0.7739 (tm-30) REVERT: G 131 ARG cc_start: 0.8964 (mtp85) cc_final: 0.8572 (mtp85) REVERT: H 43 VAL cc_start: 0.8204 (t) cc_final: 0.7909 (t) REVERT: H 49 LEU cc_start: 0.7972 (mp) cc_final: 0.7676 (mm) REVERT: H 53 GLU cc_start: 0.9333 (mt-10) cc_final: 0.9000 (mt-10) outliers start: 22 outliers final: 15 residues processed: 245 average time/residue: 0.1180 time to fit residues: 36.9366 Evaluate side-chains 246 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 229 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 59 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 30 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.057057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.040236 restraints weight = 55601.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.041539 restraints weight = 27773.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.042376 restraints weight = 18630.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.042888 restraints weight = 14716.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.043162 restraints weight = 12863.140| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9362 Z= 0.219 Angle : 0.768 10.953 13488 Z= 0.433 Chirality : 0.044 0.301 1549 Planarity : 0.006 0.075 1004 Dihedral : 31.171 149.444 2840 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.26 % Allowed : 33.20 % Favored : 61.54 % 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: 1.08 (0.33), residues: 563 helix: 1.20 (0.23), residues: 463 sheet: None (None), residues: 0 loop : -1.37 (0.48), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 92 TYR 0.026 0.002 TYR E 99 PHE 0.016 0.002 PHE G 67 HIS 0.004 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.22 ( 9362) covalent geometry : angle 0.76800 / 0.43 (13488) hydrogen bonds : bond 0.06507 / 4.33 ( 580) hydrogen bonds : angle 3.70576 / 2.72 ( 1477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8279 (mm) REVERT: A 90 MET cc_start: 0.8754 (tmm) cc_final: 0.8297 (tmm) REVERT: A 105 GLU cc_start: 0.8947 (tp30) cc_final: 0.8645 (tm-30) REVERT: A 112 ILE cc_start: 0.9736 (tp) cc_final: 0.9426 (pt) REVERT: A 120 MET cc_start: 0.8699 (mtm) cc_final: 0.8266 (mtm) REVERT: B 44 LYS cc_start: 0.9080 (mmmt) cc_final: 0.8782 (mmmt) REVERT: B 53 GLU cc_start: 0.9389 (tp30) cc_final: 0.8953 (tp30) REVERT: B 63 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8967 (mm-30) REVERT: B 68 ASP cc_start: 0.8420 (t70) cc_final: 0.8123 (t0) REVERT: B 86 VAL cc_start: 0.9580 (OUTLIER) cc_final: 0.9377 (p) REVERT: B 91 LYS cc_start: 0.9435 (mmmm) cc_final: 0.9187 (mmmm) REVERT: B 92 ARG cc_start: 0.8681 (ptm-80) cc_final: 0.8335 (ttp80) REVERT: C 70 LEU cc_start: 0.9422 (tt) cc_final: 0.9097 (tt) REVERT: C 73 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8581 (tm-30) REVERT: C 77 ASP cc_start: 0.9048 (t70) cc_final: 0.8763 (t0) REVERT: C 85 GLN cc_start: 0.9417 (OUTLIER) cc_final: 0.8297 (mt0) REVERT: C 105 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8740 (mm-30) REVERT: C 125 GLN cc_start: 0.9242 (mt0) cc_final: 0.8921 (mp10) REVERT: C 129 ARG cc_start: 0.9245 (tpp80) cc_final: 0.8864 (ttp80) REVERT: D 53 GLU cc_start: 0.9213 (tp30) cc_final: 0.8879 (tp30) REVERT: D 79 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8589 (mmmm) REVERT: E 73 GLU cc_start: 0.8782 (tt0) cc_final: 0.8566 (tm-30) REVERT: E 76 GLN cc_start: 0.9328 (pt0) cc_final: 0.8878 (pp30) REVERT: E 79 LYS cc_start: 0.8327 (tptt) cc_final: 0.8113 (tptp) REVERT: E 115 LYS cc_start: 0.9614 (mmmm) cc_final: 0.9382 (mmmm) REVERT: E 120 MET cc_start: 0.8676 (mmm) cc_final: 0.8427 (mmm) REVERT: E 129 ARG cc_start: 0.8907 (mmm160) cc_final: 0.8369 (mmm160) REVERT: F 31 LYS cc_start: 0.9327 (ttpp) cc_final: 0.9102 (ttmm) REVERT: F 44 LYS cc_start: 0.9492 (OUTLIER) cc_final: 0.9111 (mmmm) REVERT: F 52 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8190 (tm-30) REVERT: F 79 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8590 (mtmm) REVERT: F 80 THR cc_start: 0.9444 (m) cc_final: 0.8859 (p) REVERT: G 131 ARG cc_start: 0.8985 (mtp85) cc_final: 0.8680 (mtp85) REVERT: H 43 VAL cc_start: 0.8204 (t) cc_final: 0.7885 (t) REVERT: H 49 LEU cc_start: 0.8192 (mp) cc_final: 0.7953 (mm) REVERT: H 50 ILE cc_start: 0.8799 (pt) cc_final: 0.8452 (pt) REVERT: H 53 GLU cc_start: 0.9361 (mt-10) cc_final: 0.9051 (mt-10) outliers start: 26 outliers final: 17 residues processed: 235 average time/residue: 0.1256 time to fit residues: 37.7568 Evaluate side-chains 242 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 59 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 15 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.057857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.041296 restraints weight = 53655.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.042593 restraints weight = 26350.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.043488 restraints weight = 17555.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.043928 restraints weight = 13660.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.044273 restraints weight = 12006.607| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9362 Z= 0.179 Angle : 0.783 17.742 13488 Z= 0.435 Chirality : 0.044 0.312 1549 Planarity : 0.005 0.072 1004 Dihedral : 31.187 150.988 2840 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.25 % Allowed : 35.43 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.12 (0.33), residues: 563 helix: 1.22 (0.23), residues: 462 sheet: None (None), residues: 0 loop : -1.32 (0.48), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 128 TYR 0.024 0.002 TYR H 72 PHE 0.018 0.002 PHE G 78 HIS 0.003 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 ( 9362) covalent geometry : angle 0.78307 / 0.44 (13488) hydrogen bonds : bond 0.05917 / 3.91 ( 580) hydrogen bonds : angle 3.63486 / 2.69 ( 1477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8325 (mm) REVERT: A 90 MET cc_start: 0.8723 (tmm) cc_final: 0.8145 (tmm) REVERT: A 105 GLU cc_start: 0.8946 (tp30) cc_final: 0.8655 (tm-30) REVERT: A 112 ILE cc_start: 0.9708 (tp) cc_final: 0.9394 (pt) REVERT: A 120 MET cc_start: 0.8688 (mtm) cc_final: 0.8238 (mtm) REVERT: A 125 GLN cc_start: 0.9322 (mt0) cc_final: 0.8964 (mm-40) REVERT: B 44 LYS cc_start: 0.9079 (mmmt) cc_final: 0.8779 (mmmt) REVERT: B 63 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8945 (mm-30) REVERT: B 68 ASP cc_start: 0.8409 (t70) cc_final: 0.8074 (t0) REVERT: B 86 VAL cc_start: 0.9568 (t) cc_final: 0.9365 (p) REVERT: B 91 LYS cc_start: 0.9447 (mmmm) cc_final: 0.9181 (mmmm) REVERT: B 92 ARG cc_start: 0.8689 (ptm-80) cc_final: 0.8334 (ttp80) REVERT: C 73 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8570 (tm-30) REVERT: C 77 ASP cc_start: 0.9035 (t70) cc_final: 0.8766 (t0) REVERT: C 85 GLN cc_start: 0.9393 (OUTLIER) cc_final: 0.8310 (mt0) REVERT: C 105 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8717 (mm-30) REVERT: C 125 GLN cc_start: 0.9249 (mt0) cc_final: 0.8923 (mp10) REVERT: C 129 ARG cc_start: 0.9249 (tpp80) cc_final: 0.8763 (ttp80) REVERT: D 53 GLU cc_start: 0.9208 (tp30) cc_final: 0.8810 (tp30) REVERT: D 79 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8526 (mmmm) REVERT: E 73 GLU cc_start: 0.8756 (tt0) cc_final: 0.8523 (tm-30) REVERT: E 76 GLN cc_start: 0.9308 (pt0) cc_final: 0.8909 (pp30) REVERT: E 115 LYS cc_start: 0.9634 (mmmm) cc_final: 0.9396 (mmmm) REVERT: E 120 MET cc_start: 0.8684 (mmm) cc_final: 0.8157 (mmm) REVERT: E 129 ARG cc_start: 0.8910 (mmm160) cc_final: 0.8350 (mmm160) REVERT: F 31 LYS cc_start: 0.9320 (ttpp) cc_final: 0.9088 (ttmm) REVERT: F 44 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9200 (mmmm) REVERT: F 52 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8173 (tm-30) REVERT: F 79 LYS cc_start: 0.9057 (mtpp) cc_final: 0.8557 (mtmm) REVERT: F 80 THR cc_start: 0.9398 (m) cc_final: 0.8741 (p) REVERT: G 131 ARG cc_start: 0.9017 (mtp85) cc_final: 0.8691 (mtp85) REVERT: H 43 VAL cc_start: 0.8211 (t) cc_final: 0.7903 (t) REVERT: H 49 LEU cc_start: 0.8110 (mp) cc_final: 0.7832 (mm) REVERT: H 53 GLU cc_start: 0.9360 (mt-10) cc_final: 0.9057 (mt-10) outliers start: 21 outliers final: 14 residues processed: 237 average time/residue: 0.1214 time to fit residues: 36.8131 Evaluate side-chains 244 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 58 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 74 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.057134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.040545 restraints weight = 54251.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.041827 restraints weight = 26868.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.042645 restraints weight = 17882.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.043067 restraints weight = 14089.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.043387 restraints weight = 12477.379| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9362 Z= 0.192 Angle : 0.792 17.991 13488 Z= 0.440 Chirality : 0.043 0.308 1549 Planarity : 0.005 0.063 1004 Dihedral : 31.207 151.309 2840 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.66 % Allowed : 35.22 % Favored : 60.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.33), residues: 563 helix: 1.35 (0.23), residues: 462 sheet: None (None), residues: 0 loop : -1.27 (0.48), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 67 TYR 0.031 0.002 TYR H 72 PHE 0.026 0.002 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 ( 9362) covalent geometry : angle 0.79230 / 0.44 (13488) hydrogen bonds : bond 0.06031 / 4.00 ( 580) hydrogen bonds : angle 3.62277 / 2.67 ( 1477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8292 (mm) REVERT: A 90 MET cc_start: 0.8636 (tmm) cc_final: 0.8136 (tmm) REVERT: A 94 GLU cc_start: 0.9022 (tt0) cc_final: 0.8360 (tm-30) REVERT: A 105 GLU cc_start: 0.8939 (tp30) cc_final: 0.8639 (tm-30) REVERT: A 112 ILE cc_start: 0.9709 (tp) cc_final: 0.9405 (pt) REVERT: A 120 MET cc_start: 0.8734 (mtm) cc_final: 0.8347 (mtm) REVERT: A 125 GLN cc_start: 0.9337 (mt0) cc_final: 0.8978 (mm-40) REVERT: B 44 LYS cc_start: 0.9108 (mmmt) cc_final: 0.8793 (mmmt) REVERT: B 68 ASP cc_start: 0.8450 (t70) cc_final: 0.8112 (t0) REVERT: B 91 LYS cc_start: 0.9445 (mmmm) cc_final: 0.9173 (mmmm) REVERT: B 92 ARG cc_start: 0.8702 (ptm-80) cc_final: 0.8376 (ttp80) REVERT: C 73 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8610 (tm-30) REVERT: C 77 ASP cc_start: 0.9037 (t70) cc_final: 0.8756 (t0) REVERT: C 85 GLN cc_start: 0.9401 (mt0) cc_final: 0.8328 (mt0) REVERT: C 93 GLN cc_start: 0.9046 (tt0) cc_final: 0.8841 (tt0) REVERT: C 105 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8716 (mm-30) REVERT: C 125 GLN cc_start: 0.9251 (mt0) cc_final: 0.8839 (mp10) REVERT: C 129 ARG cc_start: 0.9248 (tpp80) cc_final: 0.8796 (ttp80) REVERT: D 53 GLU cc_start: 0.9197 (tp30) cc_final: 0.8816 (tp30) REVERT: D 79 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8581 (mmmm) REVERT: E 73 GLU cc_start: 0.8767 (tt0) cc_final: 0.8509 (tm-30) REVERT: E 76 GLN cc_start: 0.9324 (pt0) cc_final: 0.8913 (pp30) REVERT: E 115 LYS cc_start: 0.9632 (mmmm) cc_final: 0.9394 (mmmm) REVERT: E 120 MET cc_start: 0.8699 (mmm) cc_final: 0.8183 (mmm) REVERT: E 129 ARG cc_start: 0.8932 (mmm160) cc_final: 0.8358 (mmm160) REVERT: F 31 LYS cc_start: 0.9326 (ttpp) cc_final: 0.9072 (ttmm) REVERT: F 35 ARG cc_start: 0.9374 (ttp80) cc_final: 0.8911 (ttm-80) REVERT: F 44 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9098 (mmmm) REVERT: F 52 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8158 (tm-30) REVERT: F 79 LYS cc_start: 0.9052 (mtpp) cc_final: 0.8559 (mtmm) REVERT: F 80 THR cc_start: 0.9447 (m) cc_final: 0.8787 (p) REVERT: H 43 VAL cc_start: 0.8213 (t) cc_final: 0.7920 (t) REVERT: H 49 LEU cc_start: 0.8057 (mp) cc_final: 0.7817 (mm) REVERT: H 50 ILE cc_start: 0.8747 (pt) cc_final: 0.8402 (pt) REVERT: H 53 GLU cc_start: 0.9363 (mt-10) cc_final: 0.9065 (mt-10) outliers start: 23 outliers final: 17 residues processed: 237 average time/residue: 0.1163 time to fit residues: 35.3069 Evaluate side-chains 245 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** 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 = 0.3576 r_free = 0.3576 target = 0.057439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.040873 restraints weight = 55547.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.042146 restraints weight = 27543.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.042964 restraints weight = 18498.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.043455 restraints weight = 14604.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.043717 restraints weight = 12755.364| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9362 Z= 0.179 Angle : 0.804 18.683 13488 Z= 0.443 Chirality : 0.044 0.313 1549 Planarity : 0.005 0.063 1004 Dihedral : 31.217 152.375 2840 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.64 % Allowed : 36.64 % Favored : 59.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.33), residues: 563 helix: 1.28 (0.23), residues: 463 sheet: None (None), residues: 0 loop : -1.19 (0.49), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 78 TYR 0.032 0.002 TYR H 72 PHE 0.027 0.002 PHE G 78 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 ( 9362) covalent geometry : angle 0.80359 / 0.44 (13488) hydrogen bonds : bond 0.05827 / 3.85 ( 580) hydrogen bonds : angle 3.59884 / 2.65 ( 1477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 232 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8277 (mm) REVERT: A 90 MET cc_start: 0.8637 (tmm) cc_final: 0.8139 (tmm) REVERT: A 94 GLU cc_start: 0.9108 (tt0) cc_final: 0.7530 (tm-30) REVERT: A 105 GLU cc_start: 0.8889 (tp30) cc_final: 0.8435 (tp30) REVERT: A 112 ILE cc_start: 0.9695 (tp) cc_final: 0.9403 (pt) REVERT: A 120 MET cc_start: 0.8654 (mtm) cc_final: 0.8242 (mtm) REVERT: A 125 GLN cc_start: 0.9318 (mt0) cc_final: 0.8982 (mm-40) REVERT: B 44 LYS cc_start: 0.9083 (mmmt) cc_final: 0.8779 (mmmt) REVERT: B 63 GLU cc_start: 0.9315 (mm-30) cc_final: 0.9095 (mm-30) REVERT: B 68 ASP cc_start: 0.8451 (t70) cc_final: 0.8105 (t0) REVERT: B 77 LYS cc_start: 0.9096 (tppt) cc_final: 0.8470 (mppt) REVERT: B 91 LYS cc_start: 0.9427 (mmmm) cc_final: 0.9158 (mmmm) REVERT: B 92 ARG cc_start: 0.8702 (ptm-80) cc_final: 0.8371 (ttp80) REVERT: C 73 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8616 (tm-30) REVERT: C 77 ASP cc_start: 0.9029 (t70) cc_final: 0.8749 (t0) REVERT: C 85 GLN cc_start: 0.9386 (mt0) cc_final: 0.8339 (mt0) REVERT: C 105 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8715 (mm-30) REVERT: C 125 GLN cc_start: 0.9219 (mt0) cc_final: 0.8824 (mp10) REVERT: C 129 ARG cc_start: 0.9174 (tpp80) cc_final: 0.8726 (ttp80) REVERT: D 53 GLU cc_start: 0.9100 (tp30) cc_final: 0.8734 (tp30) REVERT: D 79 LYS cc_start: 0.8865 (mmmt) cc_final: 0.8579 (mmmm) REVERT: E 76 GLN cc_start: 0.9314 (pt0) cc_final: 0.8883 (pp30) REVERT: E 115 LYS cc_start: 0.9635 (mmmm) cc_final: 0.9398 (mmmm) REVERT: E 120 MET cc_start: 0.8711 (mmm) cc_final: 0.8202 (mmm) REVERT: E 129 ARG cc_start: 0.8936 (mmm160) cc_final: 0.8351 (mmm160) REVERT: F 31 LYS cc_start: 0.9332 (ttpp) cc_final: 0.9076 (ttmm) REVERT: F 35 ARG cc_start: 0.9371 (ttp80) cc_final: 0.8881 (ttm-80) REVERT: F 44 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.9088 (mmmm) REVERT: F 52 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8107 (tm-30) REVERT: F 79 LYS cc_start: 0.9086 (mtpp) cc_final: 0.8578 (mtmm) REVERT: F 80 THR cc_start: 0.9447 (m) cc_final: 0.8787 (p) REVERT: G 131 ARG cc_start: 0.9070 (mtp-110) cc_final: 0.8639 (mtp85) REVERT: H 43 VAL cc_start: 0.8274 (t) cc_final: 0.7981 (t) REVERT: H 49 LEU cc_start: 0.8101 (mp) cc_final: 0.7863 (mm) REVERT: H 50 ILE cc_start: 0.8786 (pt) cc_final: 0.8463 (pt) REVERT: H 53 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9000 (mt-10) outliers start: 18 outliers final: 14 residues processed: 237 average time/residue: 0.1135 time to fit residues: 34.2626 Evaluate side-chains 239 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 78 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 59 optimal weight: 10.0000 chunk 65 optimal weight: 40.0000 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.057696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.041186 restraints weight = 52813.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.042476 restraints weight = 25786.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.043315 restraints weight = 17052.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.043829 restraints weight = 13335.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.044092 restraints weight = 11583.537| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9362 Z= 0.187 Angle : 0.825 18.979 13488 Z= 0.452 Chirality : 0.045 0.312 1549 Planarity : 0.009 0.224 1004 Dihedral : 31.228 152.657 2840 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.25 % Allowed : 36.64 % Favored : 59.11 % 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: 1.18 (0.34), residues: 563 helix: 1.25 (0.23), residues: 463 sheet: None (None), residues: 0 loop : -1.20 (0.51), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG H 40 TYR 0.031 0.002 TYR H 72 PHE 0.054 0.002 PHE G 78 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 ( 9362) covalent geometry : angle 0.82507 / 0.45 (13488) hydrogen bonds : bond 0.05870 / 3.89 ( 580) hydrogen bonds : angle 3.61850 / 2.65 ( 1477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1820.77 seconds wall clock time: 31 minutes 53.60 seconds (1913.60 seconds total)