Starting phenix.real_space_refine on Fri Sep 11 21:46:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fq5_4297/09_2026/6fq5_4297.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fq5_4297/09_2026/6fq5_4297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6fq5_4297/09_2026/6fq5_4297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fq5_4297/09_2026/6fq5_4297.map" model { file = "/net/cci-nas-00/data/ceres_data/6fq5_4297/09_2026/6fq5_4297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fq5_4297/09_2026/6fq5_4297.cif" } resolution = 3.8 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= 0.003 sd= 0.031 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 294 5.49 5 S 12 5.16 5 C 6741 2.51 5 N 2303 2.21 5 O 2843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12193 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 2.68, per 1000 atoms: 0.22 Number of scatterers: 12193 At special positions: 0 Unit cell: (78.4, 120.4, 113.4, 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 12 16.00 P 294 15.00 O 2843 8.00 N 2303 7.00 C 6741 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: 0.99 Conformation dependent library (CDL) restraints added in 330.9 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1454 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 71.8% alpha, 2.8% beta 146 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.214A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.524A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.561A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.519A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.530A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.457A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.725A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.271A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.566A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.688A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.515A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.437A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.728A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.606A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.605A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.916A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.379A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.964A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.336A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 403 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 375 hydrogen bonds 750 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1746 1.32 - 1.44: 4620 1.44 - 1.56: 6033 1.56 - 1.68: 587 1.68 - 1.80: 22 Bond restraints: 13008 Sorted by residual: bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.435 1.499 -0.064 1.30e-02 5.92e+03 2.42e+01 bond pdb=" C3' DT I 35 " pdb=" C2' DT I 35 " ideal model delta sigma weight residual 1.516 1.551 -0.035 8.00e-03 1.56e+04 1.95e+01 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.435 1.488 -0.053 1.30e-02 5.92e+03 1.65e+01 bond pdb=" C3' DC J 69 " pdb=" C2' DC J 69 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.63e+01 bond pdb=" C3' DC J 6 " pdb=" O3' DC J 6 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.54e+01 ... (remaining 13003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 17751 2.38 - 4.76: 980 4.76 - 7.14: 71 7.14 - 9.51: 14 9.51 - 11.89: 6 Bond angle restraints: 18822 Sorted by residual: angle pdb=" O4' DA J -9 " pdb=" C4' DA J -9 " pdb=" C3' DA J -9 " ideal model delta sigma weight residual 106.00 101.60 4.40 6.00e-01 2.78e+00 5.39e+01 angle pdb=" O4' DT I -57 " pdb=" C4' DT I -57 " pdb=" C3' DT I -57 " ideal model delta sigma weight residual 106.00 102.21 3.79 6.00e-01 2.78e+00 3.98e+01 angle pdb=" O4' DG I 56 " pdb=" C4' DG I 56 " pdb=" C3' DG I 56 " ideal model delta sigma weight residual 106.00 102.40 3.60 6.00e-01 2.78e+00 3.60e+01 angle pdb=" N3 DT I 54 " pdb=" C4 DT I 54 " pdb=" O4 DT I 54 " ideal model delta sigma weight residual 119.90 123.08 -3.18 6.00e-01 2.78e+00 2.81e+01 angle pdb=" O4' DG I -36 " pdb=" C4' DG I -36 " pdb=" C3' DG I -36 " ideal model delta sigma weight residual 106.00 102.82 3.18 6.00e-01 2.78e+00 2.80e+01 ... (remaining 18817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.26: 5478 34.26 - 68.51: 1560 68.51 - 102.77: 37 102.77 - 137.02: 3 137.02 - 171.28: 3 Dihedral angle restraints: 7081 sinusoidal: 4831 harmonic: 2250 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 48.72 171.28 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 54.95 165.05 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" CA ARG D 27 " pdb=" C ARG D 27 " pdb=" N LYS D 28 " pdb=" CA LYS D 28 " ideal model delta harmonic sigma weight residual 180.00 -161.24 -18.76 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 7078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1539 0.065 - 0.130: 518 0.130 - 0.194: 72 0.194 - 0.259: 10 0.259 - 0.324: 4 Chirality restraints: 2143 Sorted by residual: chirality pdb=" CA PRO C 80 " pdb=" N PRO C 80 " pdb=" C PRO C 80 " pdb=" CB PRO C 80 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA PRO G 80 " pdb=" N PRO G 80 " pdb=" C PRO G 80 " pdb=" CB PRO G 80 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CG LEU B 22 " pdb=" CB LEU B 22 " pdb=" CD1 LEU B 22 " pdb=" CD2 LEU B 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 2140 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 64 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C ASN B 64 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN B 64 " -0.028 2.00e-02 2.50e+03 pdb=" N VAL B 65 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 105 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C LYS D 105 " 0.067 2.00e-02 2.50e+03 pdb=" O LYS D 105 " -0.025 2.00e-02 2.50e+03 pdb=" N HIS D 106 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR F 72 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C TYR F 72 " 0.063 2.00e-02 2.50e+03 pdb=" O TYR F 72 " -0.024 2.00e-02 2.50e+03 pdb=" N THR F 73 " -0.021 2.00e-02 2.50e+03 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2276 2.78 - 3.31: 10754 3.31 - 3.84: 25082 3.84 - 4.37: 27703 4.37 - 4.90: 39345 Nonbonded interactions: 105160 Sorted by model distance: nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.253 3.040 nonbonded pdb=" OG1 THR H 29 " pdb=" OP1 DT J 30 " model vdw 2.299 3.040 nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.329 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.340 3.040 nonbonded pdb=" OE2 GLU E 133 " pdb=" NH2 ARG F 95 " model vdw 2.341 3.120 ... (remaining 105155 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 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 18 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.380 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 : 0.009 0.077 13008 Z= 0.743 Angle : 1.201 11.893 18822 Z= 0.932 Chirality : 0.063 0.324 2143 Planarity : 0.008 0.042 1360 Dihedral : 28.680 171.275 5627 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.31 % Allowed : 1.55 % Favored : 98.15 % 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: -1.55 (0.25), residues: 758 helix: -0.74 (0.18), residues: 544 sheet: None (None), residues: 0 loop : -1.39 (0.36), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 30 TYR 0.029 0.004 TYR A 54 PHE 0.037 0.005 PHE G 25 HIS 0.018 0.003 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00890 / 0.74 (13008) covalent geometry : angle 1.20148 / 0.93 (18822) hydrogen bonds : bond 0.13266 / 9.09 ( 778) hydrogen bonds : angle 4.99491 / 3.73 ( 1938) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 390 time to evaluate : 0.320 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: A 38 PRO cc_start: 0.6958 (Cg_exo) cc_final: 0.6727 (Cg_endo) REVERT: A 51 ILE cc_start: 0.9322 (mt) cc_final: 0.9023 (mt) REVERT: A 56 LYS cc_start: 0.8721 (tttt) cc_final: 0.8483 (tttp) REVERT: A 58 THR cc_start: 0.7519 (p) cc_final: 0.7269 (t) REVERT: B 24 ASP cc_start: 0.6823 (m-30) cc_final: 0.6106 (p0) REVERT: B 59 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8405 (ttpp) REVERT: B 60 VAL cc_start: 0.9172 (t) cc_final: 0.8796 (t) REVERT: B 63 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7619 (mt-10) REVERT: C 84 GLN cc_start: 0.7358 (tp40) cc_final: 0.6998 (tp40) REVERT: C 113 SER cc_start: 0.9098 (m) cc_final: 0.8849 (p) REVERT: D 31 LYS cc_start: 0.7934 (mttt) cc_final: 0.7571 (pptt) REVERT: D 40 LYS cc_start: 0.8872 (mttt) cc_final: 0.8517 (mtpt) REVERT: D 43 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8763 (mmmt) REVERT: D 76 ARG cc_start: 0.8594 (mtt90) cc_final: 0.8237 (ttm110) REVERT: D 80 TYR cc_start: 0.7159 (m-10) cc_final: 0.6909 (m-10) REVERT: D 106 HIS cc_start: 0.8580 (m-70) cc_final: 0.7410 (m-70) REVERT: D 109 SER cc_start: 0.9321 (t) cc_final: 0.8810 (p) REVERT: E 51 ILE cc_start: 0.9352 (mt) cc_final: 0.8929 (mt) REVERT: E 58 THR cc_start: 0.7748 (p) cc_final: 0.7533 (t) REVERT: E 67 PHE cc_start: 0.8391 (t80) cc_final: 0.7795 (t80) REVERT: F 59 LYS cc_start: 0.8703 (tttm) cc_final: 0.8158 (ttpp) REVERT: F 63 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7459 (mt-10) REVERT: F 82 THR cc_start: 0.8478 (p) cc_final: 0.8257 (p) REVERT: F 90 LEU cc_start: 0.9224 (mt) cc_final: 0.8893 (mp) REVERT: F 100 PHE cc_start: 0.7196 (m-80) cc_final: 0.6352 (m-80) REVERT: G 84 GLN cc_start: 0.7459 (tp40) cc_final: 0.6756 (tp40) REVERT: G 113 SER cc_start: 0.8966 (m) cc_final: 0.8642 (p) REVERT: H 40 LYS cc_start: 0.8837 (mttt) cc_final: 0.8611 (mtpt) REVERT: H 73 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8520 (mm-30) REVERT: H 86 ILE cc_start: 0.8867 (mt) cc_final: 0.8610 (tp) REVERT: H 106 HIS cc_start: 0.9053 (m-70) cc_final: 0.7621 (m170) REVERT: H 109 SER cc_start: 0.9317 (m) cc_final: 0.8827 (p) outliers start: 2 outliers final: 0 residues processed: 392 average time/residue: 0.1403 time to fit residues: 74.0064 Evaluate side-chains 217 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 108 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 110 ASN D 60 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN E 113 HIS G 73 ASN G 110 ASN H 44 GLN H 46 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.065936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.056503 restraints weight = 65220.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.058017 restraints weight = 32944.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.059037 restraints weight = 20383.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.059682 restraints weight = 14306.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.060204 restraints weight = 11256.641| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13008 Z= 0.208 Angle : 0.828 8.482 18822 Z= 0.477 Chirality : 0.055 0.402 2143 Planarity : 0.006 0.056 1360 Dihedral : 32.805 169.014 4077 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.86 % Allowed : 19.63 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.29), residues: 758 helix: 1.11 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.83 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 45 TYR 0.031 0.003 TYR E 54 PHE 0.027 0.002 PHE A 67 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.21 (13008) covalent geometry : angle 0.82764 / 0.48 (18822) hydrogen bonds : bond 0.06647 / 4.43 ( 778) hydrogen bonds : angle 3.76392 / 2.81 ( 1938) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9065 (tttt) cc_final: 0.8850 (tttm) REVERT: A 93 GLN cc_start: 0.8348 (tp40) cc_final: 0.8148 (tp40) REVERT: B 59 LYS cc_start: 0.8784 (ttpt) cc_final: 0.8112 (ttpp) REVERT: B 60 VAL cc_start: 0.9295 (t) cc_final: 0.8923 (t) REVERT: B 63 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7559 (mt-10) REVERT: B 90 LEU cc_start: 0.9253 (mt) cc_final: 0.8989 (mp) REVERT: C 50 TYR cc_start: 0.8647 (t80) cc_final: 0.8334 (t80) REVERT: C 84 GLN cc_start: 0.8215 (tp40) cc_final: 0.7835 (mm-40) REVERT: C 113 SER cc_start: 0.8987 (m) cc_final: 0.8683 (p) REVERT: D 31 LYS cc_start: 0.7969 (mttt) cc_final: 0.7521 (pptt) REVERT: D 40 LYS cc_start: 0.9290 (mttt) cc_final: 0.8891 (mtpt) REVERT: D 73 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8578 (mm-30) REVERT: D 76 ARG cc_start: 0.8879 (mtt90) cc_final: 0.8353 (ttm110) REVERT: D 106 HIS cc_start: 0.9042 (m-70) cc_final: 0.8707 (m170) REVERT: E 58 THR cc_start: 0.7750 (p) cc_final: 0.7484 (t) REVERT: E 123 ASP cc_start: 0.8660 (m-30) cc_final: 0.8337 (t70) REVERT: E 125 GLN cc_start: 0.8751 (mt0) cc_final: 0.8379 (mm-40) REVERT: F 51 TYR cc_start: 0.7402 (m-80) cc_final: 0.6764 (m-80) REVERT: F 54 THR cc_start: 0.9367 (m) cc_final: 0.8927 (p) REVERT: F 71 THR cc_start: 0.9001 (m) cc_final: 0.8766 (p) REVERT: G 113 SER cc_start: 0.8738 (m) cc_final: 0.8375 (p) REVERT: H 40 LYS cc_start: 0.9290 (mttt) cc_final: 0.9054 (mtpt) REVERT: H 73 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8606 (mm-30) REVERT: H 86 ILE cc_start: 0.8837 (mt) cc_final: 0.8601 (tt) REVERT: H 90 GLU cc_start: 0.8422 (mp0) cc_final: 0.7922 (mp0) REVERT: H 106 HIS cc_start: 0.8974 (m-70) cc_final: 0.8085 (m90) REVERT: H 109 SER cc_start: 0.9407 (m) cc_final: 0.8974 (p) REVERT: H 110 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8028 (mm-30) outliers start: 25 outliers final: 13 residues processed: 264 average time/residue: 0.1021 time to fit residues: 39.6814 Evaluate side-chains 225 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 212 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 98 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 14 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS B 18 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN G 38 ASN G 110 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.066480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.057026 restraints weight = 63270.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.058565 restraints weight = 30744.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.059589 restraints weight = 18545.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.060248 restraints weight = 12923.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.060676 restraints weight = 10105.457| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13008 Z= 0.183 Angle : 0.737 8.266 18822 Z= 0.430 Chirality : 0.051 0.382 2143 Planarity : 0.005 0.046 1360 Dihedral : 32.576 167.228 4077 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.71 % Allowed : 19.94 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.29), residues: 758 helix: 1.52 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.74 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 69 TYR 0.025 0.002 TYR C 57 PHE 0.017 0.002 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.18 (13008) covalent geometry : angle 0.73660 / 0.43 (18822) hydrogen bonds : bond 0.05938 / 3.98 ( 778) hydrogen bonds : angle 3.54772 / 2.65 ( 1938) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8954 (m-30) cc_final: 0.8678 (m-30) REVERT: B 40 ARG cc_start: 0.8256 (ttp-170) cc_final: 0.6688 (tpp80) REVERT: B 59 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8000 (ttpp) REVERT: B 60 VAL cc_start: 0.9219 (t) cc_final: 0.8725 (p) REVERT: B 63 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7503 (mt-10) REVERT: B 90 LEU cc_start: 0.9235 (mt) cc_final: 0.8964 (mp) REVERT: C 113 SER cc_start: 0.8946 (m) cc_final: 0.8617 (p) REVERT: D 31 LYS cc_start: 0.7948 (mttt) cc_final: 0.7476 (pptt) REVERT: D 39 TYR cc_start: 0.8609 (t80) cc_final: 0.7998 (t80) REVERT: D 40 LYS cc_start: 0.9248 (mttt) cc_final: 0.8833 (mtpt) REVERT: D 43 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8753 (mmmt) REVERT: D 106 HIS cc_start: 0.8966 (m-70) cc_final: 0.8447 (m170) REVERT: D 110 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8221 (mm-30) REVERT: E 50 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7507 (tp30) REVERT: E 58 THR cc_start: 0.7813 (p) cc_final: 0.7535 (t) REVERT: E 85 GLN cc_start: 0.8933 (mt0) cc_final: 0.8605 (pt0) REVERT: E 120 MET cc_start: 0.5461 (mtt) cc_final: 0.4878 (mtt) REVERT: E 123 ASP cc_start: 0.8819 (m-30) cc_final: 0.8415 (m-30) REVERT: E 125 GLN cc_start: 0.8698 (mt0) cc_final: 0.8392 (mm-40) REVERT: E 133 GLU cc_start: 0.7140 (mp0) cc_final: 0.6059 (mt-10) REVERT: G 34 LEU cc_start: 0.9524 (tp) cc_final: 0.9176 (tt) REVERT: H 40 LYS cc_start: 0.9325 (mttt) cc_final: 0.9079 (mtmt) REVERT: H 73 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8610 (mm-30) REVERT: H 106 HIS cc_start: 0.9048 (m-70) cc_final: 0.8544 (m90) REVERT: H 109 SER cc_start: 0.9479 (m) cc_final: 0.9176 (p) outliers start: 24 outliers final: 16 residues processed: 233 average time/residue: 0.0934 time to fit residues: 32.8794 Evaluate side-chains 207 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 65 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 32 optimal weight: 4.9990 chunk 90 optimal weight: 40.0000 chunk 13 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 93 optimal weight: 40.0000 chunk 11 optimal weight: 0.6980 chunk 84 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 89 optimal weight: 40.0000 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.065340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.055868 restraints weight = 64463.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.057351 restraints weight = 31868.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.058379 restraints weight = 19693.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.059046 restraints weight = 13743.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.059546 restraints weight = 10746.283| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13008 Z= 0.186 Angle : 0.717 8.449 18822 Z= 0.422 Chirality : 0.049 0.379 2143 Planarity : 0.005 0.034 1360 Dihedral : 32.428 165.723 4077 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.09 % Allowed : 22.26 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.29), residues: 758 helix: 1.62 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -0.70 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.036 0.003 TYR D 80 PHE 0.023 0.002 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.19 (13008) covalent geometry : angle 0.71726 / 0.42 (18822) hydrogen bonds : bond 0.05836 / 3.91 ( 778) hydrogen bonds : angle 3.55052 / 2.65 ( 1938) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8561 (t80) cc_final: 0.8353 (t80) REVERT: A 73 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8202 (pp20) REVERT: A 93 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8168 (tp40) REVERT: A 123 ASP cc_start: 0.8929 (m-30) cc_final: 0.7557 (t70) REVERT: B 59 LYS cc_start: 0.8720 (ttpt) cc_final: 0.7980 (ttpp) REVERT: B 60 VAL cc_start: 0.9270 (t) cc_final: 0.8697 (p) REVERT: B 63 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7527 (mt-10) REVERT: B 90 LEU cc_start: 0.9245 (mt) cc_final: 0.8963 (mp) REVERT: C 41 GLU cc_start: 0.8519 (pt0) cc_final: 0.7826 (pp20) REVERT: C 113 SER cc_start: 0.8873 (m) cc_final: 0.8587 (p) REVERT: D 39 TYR cc_start: 0.8635 (t80) cc_final: 0.7868 (t80) REVERT: D 40 LYS cc_start: 0.9267 (mttt) cc_final: 0.8892 (mtpt) REVERT: D 43 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8819 (mmmt) REVERT: E 58 THR cc_start: 0.8000 (p) cc_final: 0.7679 (t) REVERT: E 85 GLN cc_start: 0.8822 (mt0) cc_final: 0.8442 (mp10) REVERT: E 90 MET cc_start: 0.9320 (tpp) cc_final: 0.8788 (tpp) REVERT: E 120 MET cc_start: 0.5590 (mtt) cc_final: 0.4941 (mtt) REVERT: E 123 ASP cc_start: 0.8889 (m-30) cc_final: 0.8419 (m-30) REVERT: E 125 GLN cc_start: 0.8724 (mt0) cc_final: 0.8305 (mt0) REVERT: H 40 LYS cc_start: 0.9348 (mttt) cc_final: 0.9087 (mtmt) REVERT: H 106 HIS cc_start: 0.9083 (m-70) cc_final: 0.8217 (m90) REVERT: H 109 SER cc_start: 0.9464 (m) cc_final: 0.8973 (t) REVERT: H 110 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8019 (mm-30) outliers start: 20 outliers final: 15 residues processed: 220 average time/residue: 0.0911 time to fit residues: 30.5864 Evaluate side-chains 204 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 65 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 30.0000 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 60 optimal weight: 0.0050 chunk 23 optimal weight: 3.9990 chunk 90 optimal weight: 30.0000 chunk 95 optimal weight: 30.0000 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.067042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.057401 restraints weight = 63120.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.058957 restraints weight = 31066.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.060025 restraints weight = 18879.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.060746 restraints weight = 13173.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.061271 restraints weight = 10200.314| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 13008 Z= 0.155 Angle : 0.689 9.066 18822 Z= 0.403 Chirality : 0.049 0.354 2143 Planarity : 0.004 0.034 1360 Dihedral : 32.239 164.707 4077 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.16 % Allowed : 23.49 % Favored : 74.34 % 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: 1.49 (0.29), residues: 758 helix: 1.65 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.64 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 99 TYR 0.036 0.002 TYR H 80 PHE 0.023 0.002 PHE B 61 HIS 0.003 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 (13008) covalent geometry : angle 0.68917 / 0.40 (18822) hydrogen bonds : bond 0.04805 / 3.25 ( 778) hydrogen bonds : angle 3.44088 / 2.57 ( 1938) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8480 (t80) cc_final: 0.8278 (t80) REVERT: A 93 GLN cc_start: 0.8383 (tp-100) cc_final: 0.7951 (tp40) REVERT: A 123 ASP cc_start: 0.9070 (m-30) cc_final: 0.7915 (t0) REVERT: B 59 LYS cc_start: 0.8694 (ttpt) cc_final: 0.7947 (ttpp) REVERT: B 60 VAL cc_start: 0.9271 (t) cc_final: 0.8692 (p) REVERT: B 63 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7464 (mt-10) REVERT: B 90 LEU cc_start: 0.9188 (mt) cc_final: 0.8884 (mp) REVERT: C 50 TYR cc_start: 0.8496 (t80) cc_final: 0.8014 (t80) REVERT: C 113 SER cc_start: 0.8843 (m) cc_final: 0.8601 (p) REVERT: D 40 LYS cc_start: 0.9263 (mttt) cc_final: 0.8816 (mtmt) REVERT: E 58 THR cc_start: 0.8010 (p) cc_final: 0.7700 (t) REVERT: E 85 GLN cc_start: 0.8769 (mt0) cc_final: 0.8471 (mp10) REVERT: E 90 MET cc_start: 0.9285 (tpp) cc_final: 0.8676 (tpp) REVERT: E 93 GLN cc_start: 0.8659 (tp40) cc_final: 0.8276 (tp40) REVERT: E 123 ASP cc_start: 0.8907 (m-30) cc_final: 0.8363 (m-30) REVERT: E 125 GLN cc_start: 0.8713 (mt0) cc_final: 0.8385 (mm-40) REVERT: F 59 LYS cc_start: 0.8891 (ttpp) cc_final: 0.8466 (ttpp) REVERT: G 34 LEU cc_start: 0.9564 (tp) cc_final: 0.9200 (tt) REVERT: H 31 LYS cc_start: 0.7381 (tptp) cc_final: 0.7168 (tppt) REVERT: H 40 LYS cc_start: 0.9370 (mttt) cc_final: 0.9086 (mtmt) REVERT: H 73 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8662 (mm-30) REVERT: H 76 ARG cc_start: 0.9003 (ptp90) cc_final: 0.8787 (ptp90) REVERT: H 106 HIS cc_start: 0.9138 (m-70) cc_final: 0.7820 (m90) REVERT: H 109 SER cc_start: 0.9509 (m) cc_final: 0.9041 (p) REVERT: H 110 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8095 (mm-30) outliers start: 14 outliers final: 12 residues processed: 225 average time/residue: 0.0920 time to fit residues: 31.6412 Evaluate side-chains 195 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 65 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 30.0000 chunk 95 optimal weight: 30.0000 chunk 55 optimal weight: 1.9990 chunk 88 optimal weight: 30.0000 chunk 29 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.066187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.056737 restraints weight = 63382.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.058278 restraints weight = 31181.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.059312 restraints weight = 18966.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.059991 restraints weight = 13285.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.060565 restraints weight = 10321.040| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13008 Z= 0.164 Angle : 0.691 8.618 18822 Z= 0.402 Chirality : 0.048 0.343 2143 Planarity : 0.004 0.038 1360 Dihedral : 32.067 163.775 4077 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.02 % Allowed : 24.42 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.29), residues: 758 helix: 1.68 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.57 (0.39), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 40 TYR 0.042 0.003 TYR H 80 PHE 0.020 0.002 PHE B 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (13008) covalent geometry : angle 0.69081 / 0.40 (18822) hydrogen bonds : bond 0.05091 / 3.42 ( 778) hydrogen bonds : angle 3.45588 / 2.57 ( 1938) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8469 (tp-100) cc_final: 0.8058 (tp40) REVERT: A 123 ASP cc_start: 0.9024 (m-30) cc_final: 0.8770 (m-30) REVERT: B 59 LYS cc_start: 0.8694 (ttpt) cc_final: 0.7940 (ttpp) REVERT: B 60 VAL cc_start: 0.9225 (t) cc_final: 0.8612 (p) REVERT: B 63 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7477 (mt-10) REVERT: B 90 LEU cc_start: 0.9209 (mt) cc_final: 0.8899 (mp) REVERT: C 113 SER cc_start: 0.8848 (m) cc_final: 0.8600 (p) REVERT: D 40 LYS cc_start: 0.9268 (mttt) cc_final: 0.8876 (mtpt) REVERT: D 43 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8785 (mmmt) REVERT: E 58 THR cc_start: 0.8032 (p) cc_final: 0.7735 (t) REVERT: E 90 MET cc_start: 0.9245 (tpp) cc_final: 0.8880 (tpp) REVERT: E 93 GLN cc_start: 0.8544 (tp40) cc_final: 0.8270 (tp40) REVERT: E 120 MET cc_start: 0.5476 (mtt) cc_final: 0.4742 (mtt) REVERT: E 123 ASP cc_start: 0.8925 (m-30) cc_final: 0.8381 (m-30) REVERT: E 125 GLN cc_start: 0.8736 (mt0) cc_final: 0.8315 (mt0) REVERT: H 40 LYS cc_start: 0.9406 (mttt) cc_final: 0.9126 (mtmt) REVERT: H 73 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8695 (mm-30) REVERT: H 106 HIS cc_start: 0.9146 (m-70) cc_final: 0.7898 (m90) REVERT: H 109 SER cc_start: 0.9518 (m) cc_final: 0.9031 (p) REVERT: H 110 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8318 (mm-30) outliers start: 26 outliers final: 18 residues processed: 207 average time/residue: 0.0892 time to fit residues: 28.4884 Evaluate side-chains 199 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 99 optimal weight: 30.0000 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 82 optimal weight: 30.0000 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 80 optimal weight: 30.0000 chunk 48 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** 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 = 0.3538 r_free = 0.3538 target = 0.065051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.055602 restraints weight = 64435.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.057104 restraints weight = 32028.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.058100 restraints weight = 19656.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.058809 restraints weight = 13870.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.059240 restraints weight = 10793.345| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13008 Z= 0.188 Angle : 0.704 11.881 18822 Z= 0.410 Chirality : 0.048 0.326 2143 Planarity : 0.005 0.053 1360 Dihedral : 31.938 162.276 4077 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.02 % Allowed : 25.19 % Favored : 70.79 % 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: 1.42 (0.29), residues: 758 helix: 1.54 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.52 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.023 0.003 TYR H 37 PHE 0.027 0.002 PHE A 67 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.19 (13008) covalent geometry : angle 0.70427 / 0.41 (18822) hydrogen bonds : bond 0.05584 / 3.74 ( 778) hydrogen bonds : angle 3.53597 / 2.64 ( 1938) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8479 (tp-100) cc_final: 0.8049 (tp40) REVERT: A 123 ASP cc_start: 0.8944 (m-30) cc_final: 0.8702 (m-30) REVERT: B 59 LYS cc_start: 0.8705 (ttpt) cc_final: 0.7895 (ttpp) REVERT: B 60 VAL cc_start: 0.9233 (t) cc_final: 0.8541 (p) REVERT: B 63 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7535 (mt-10) REVERT: B 90 LEU cc_start: 0.9209 (mt) cc_final: 0.8919 (mp) REVERT: C 113 SER cc_start: 0.8832 (m) cc_final: 0.8576 (p) REVERT: D 40 LYS cc_start: 0.9268 (mttt) cc_final: 0.8899 (mtpt) REVERT: E 58 THR cc_start: 0.7988 (p) cc_final: 0.7702 (t) REVERT: E 73 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8154 (pp20) REVERT: E 90 MET cc_start: 0.9202 (tpp) cc_final: 0.8980 (tpp) REVERT: E 93 GLN cc_start: 0.8603 (tp40) cc_final: 0.8199 (tp40) REVERT: E 103 LEU cc_start: 0.9395 (tp) cc_final: 0.9166 (mm) REVERT: E 123 ASP cc_start: 0.8930 (m-30) cc_final: 0.8323 (m-30) REVERT: E 125 GLN cc_start: 0.8749 (mt0) cc_final: 0.8533 (mm-40) REVERT: F 59 LYS cc_start: 0.8732 (ttpp) cc_final: 0.8451 (ttmt) REVERT: G 50 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7987 (t80) REVERT: H 40 LYS cc_start: 0.9444 (mttt) cc_final: 0.9153 (mtmt) REVERT: H 73 GLU cc_start: 0.9222 (mm-30) cc_final: 0.8724 (mm-30) REVERT: H 106 HIS cc_start: 0.9189 (m-70) cc_final: 0.7792 (m170) REVERT: H 109 SER cc_start: 0.9527 (m) cc_final: 0.9031 (p) REVERT: H 110 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8373 (mm-30) outliers start: 26 outliers final: 20 residues processed: 198 average time/residue: 0.0840 time to fit residues: 25.9589 Evaluate side-chains 196 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 30.0000 chunk 4 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 40.0000 chunk 92 optimal weight: 30.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.065054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.056030 restraints weight = 64391.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.057508 restraints weight = 31535.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.058531 restraints weight = 19127.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.059197 restraints weight = 13258.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.059624 restraints weight = 10247.174| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13008 Z= 0.177 Angle : 0.695 9.928 18822 Z= 0.406 Chirality : 0.047 0.309 2143 Planarity : 0.005 0.051 1360 Dihedral : 31.869 161.611 4077 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.55 % Allowed : 25.50 % Favored : 70.94 % 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: 1.32 (0.29), residues: 758 helix: 1.48 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.65 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 92 TYR 0.028 0.003 TYR H 80 PHE 0.029 0.002 PHE E 67 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.18 (13008) covalent geometry : angle 0.69537 / 0.41 (18822) hydrogen bonds : bond 0.05173 / 3.45 ( 778) hydrogen bonds : angle 3.54863 / 2.65 ( 1938) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8124 (pp20) cc_final: 0.7672 (pp20) REVERT: A 123 ASP cc_start: 0.8970 (m-30) cc_final: 0.7866 (t70) REVERT: B 59 LYS cc_start: 0.8726 (ttpt) cc_final: 0.7881 (ttpp) REVERT: B 60 VAL cc_start: 0.9259 (t) cc_final: 0.8618 (p) REVERT: B 63 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7482 (mt-10) REVERT: B 90 LEU cc_start: 0.9183 (mt) cc_final: 0.8875 (mp) REVERT: C 113 SER cc_start: 0.8749 (m) cc_final: 0.8493 (p) REVERT: D 40 LYS cc_start: 0.9270 (mttt) cc_final: 0.8916 (mtpt) REVERT: D 90 GLU cc_start: 0.8601 (mp0) cc_final: 0.8130 (mp0) REVERT: E 73 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8115 (pp20) REVERT: E 85 GLN cc_start: 0.8356 (pt0) cc_final: 0.8053 (pt0) REVERT: E 93 GLN cc_start: 0.8583 (tp40) cc_final: 0.8178 (tp40) REVERT: E 103 LEU cc_start: 0.9391 (tp) cc_final: 0.9146 (mm) REVERT: E 123 ASP cc_start: 0.8905 (m-30) cc_final: 0.8417 (m-30) REVERT: E 125 GLN cc_start: 0.8749 (mt0) cc_final: 0.8276 (mt0) REVERT: F 59 LYS cc_start: 0.8745 (ttpp) cc_final: 0.8440 (ttmt) REVERT: G 50 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.8027 (t80) REVERT: H 40 LYS cc_start: 0.9430 (mttt) cc_final: 0.9145 (mtmt) REVERT: H 56 MET cc_start: 0.9133 (tpp) cc_final: 0.8838 (tpt) REVERT: H 73 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8649 (mm-30) REVERT: H 106 HIS cc_start: 0.9197 (m-70) cc_final: 0.7809 (m170) REVERT: H 109 SER cc_start: 0.9534 (m) cc_final: 0.9049 (p) REVERT: H 110 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8504 (mm-30) outliers start: 23 outliers final: 17 residues processed: 197 average time/residue: 0.0897 time to fit residues: 27.0728 Evaluate side-chains 193 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 65 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 75 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 101 optimal weight: 40.0000 chunk 45 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.065389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.055860 restraints weight = 64218.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.057342 restraints weight = 32119.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.058364 restraints weight = 19915.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.059091 restraints weight = 14129.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.059580 restraints weight = 10948.112| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13008 Z= 0.155 Angle : 0.692 9.669 18822 Z= 0.400 Chirality : 0.047 0.294 2143 Planarity : 0.004 0.053 1360 Dihedral : 31.776 161.073 4077 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.40 % Allowed : 26.43 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.40 (0.29), residues: 758 helix: 1.55 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.63 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 92 TYR 0.020 0.002 TYR B 98 PHE 0.026 0.002 PHE A 67 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 (13008) covalent geometry : angle 0.69217 / 0.40 (18822) hydrogen bonds : bond 0.04679 / 3.14 ( 778) hydrogen bonds : angle 3.44419 / 2.58 ( 1938) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8360 (pp20) cc_final: 0.7922 (pp20) REVERT: A 93 GLN cc_start: 0.8638 (tp40) cc_final: 0.8384 (tp40) REVERT: A 99 TYR cc_start: 0.8618 (t80) cc_final: 0.8337 (t80) REVERT: A 123 ASP cc_start: 0.9093 (m-30) cc_final: 0.7776 (t70) REVERT: B 59 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8237 (ttpp) REVERT: B 60 VAL cc_start: 0.9212 (t) cc_final: 0.8506 (p) REVERT: B 63 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7448 (mt-10) REVERT: B 90 LEU cc_start: 0.9132 (mt) cc_final: 0.8818 (mp) REVERT: D 40 LYS cc_start: 0.9249 (mttt) cc_final: 0.8898 (mtpt) REVERT: D 90 GLU cc_start: 0.8591 (mp0) cc_final: 0.8046 (mp0) REVERT: E 73 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8160 (pp20) REVERT: E 85 GLN cc_start: 0.8375 (pt0) cc_final: 0.8074 (pt0) REVERT: E 93 GLN cc_start: 0.8550 (tp40) cc_final: 0.8026 (tp40) REVERT: E 103 LEU cc_start: 0.9404 (tp) cc_final: 0.9198 (mm) REVERT: E 123 ASP cc_start: 0.8917 (m-30) cc_final: 0.8391 (m-30) REVERT: E 125 GLN cc_start: 0.8700 (mt0) cc_final: 0.8490 (mm-40) REVERT: F 59 LYS cc_start: 0.8876 (ttpp) cc_final: 0.8569 (ttmt) REVERT: G 50 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.8051 (t80) REVERT: G 82 HIS cc_start: 0.8871 (m90) cc_final: 0.8653 (m90) REVERT: H 40 LYS cc_start: 0.9431 (mttt) cc_final: 0.9079 (mtpt) REVERT: H 73 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8659 (mm-30) REVERT: H 76 ARG cc_start: 0.8942 (ptp90) cc_final: 0.8571 (ptp90) REVERT: H 106 HIS cc_start: 0.9218 (m-70) cc_final: 0.7842 (m170) REVERT: H 109 SER cc_start: 0.9538 (m) cc_final: 0.9061 (p) REVERT: H 110 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8507 (mm-30) outliers start: 22 outliers final: 15 residues processed: 199 average time/residue: 0.0935 time to fit residues: 28.4189 Evaluate side-chains 190 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 79 optimal weight: 30.0000 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 30.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 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 = 0.3540 r_free = 0.3540 target = 0.065091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.055835 restraints weight = 65028.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.057325 restraints weight = 32348.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.058340 restraints weight = 19859.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.059044 restraints weight = 13917.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.059514 restraints weight = 10795.414| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13008 Z= 0.171 Angle : 0.716 11.275 18822 Z= 0.411 Chirality : 0.047 0.288 2143 Planarity : 0.005 0.050 1360 Dihedral : 31.714 160.232 4077 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.78 % Allowed : 26.74 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.33 (0.29), residues: 758 helix: 1.53 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.74 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 35 TYR 0.020 0.003 TYR B 98 PHE 0.023 0.002 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (13008) covalent geometry : angle 0.71611 / 0.41 (18822) hydrogen bonds : bond 0.05071 / 3.40 ( 778) hydrogen bonds : angle 3.49753 / 2.62 ( 1938) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8362 (pp20) cc_final: 0.7913 (pp20) REVERT: A 93 GLN cc_start: 0.8606 (tp40) cc_final: 0.8284 (tp40) REVERT: A 123 ASP cc_start: 0.9065 (m-30) cc_final: 0.7789 (t70) REVERT: B 27 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7564 (mm-40) REVERT: B 90 LEU cc_start: 0.9159 (mt) cc_final: 0.8840 (mp) REVERT: D 40 LYS cc_start: 0.9241 (mttt) cc_final: 0.8877 (mtpt) REVERT: D 90 GLU cc_start: 0.8560 (mp0) cc_final: 0.8095 (mp0) REVERT: E 73 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8105 (pp20) REVERT: E 85 GLN cc_start: 0.8369 (pt0) cc_final: 0.8124 (pt0) REVERT: E 93 GLN cc_start: 0.8620 (tp40) cc_final: 0.8170 (tp40) REVERT: E 103 LEU cc_start: 0.9390 (tp) cc_final: 0.9180 (mm) REVERT: E 123 ASP cc_start: 0.8883 (m-30) cc_final: 0.8367 (m-30) REVERT: E 125 GLN cc_start: 0.8704 (mt0) cc_final: 0.8501 (mm-40) REVERT: F 59 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8581 (ttmt) REVERT: G 50 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.8047 (t80) REVERT: G 82 HIS cc_start: 0.8868 (m90) cc_final: 0.8656 (m90) REVERT: H 40 LYS cc_start: 0.9436 (mttt) cc_final: 0.9120 (mtpt) REVERT: H 73 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8719 (mm-30) REVERT: H 106 HIS cc_start: 0.9198 (m-70) cc_final: 0.7816 (m170) REVERT: H 109 SER cc_start: 0.9532 (m) cc_final: 0.9044 (p) REVERT: H 110 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8483 (mm-30) outliers start: 18 outliers final: 13 residues processed: 186 average time/residue: 0.0923 time to fit residues: 26.3654 Evaluate side-chains 182 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 40.0000 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 81 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 = 0.3555 r_free = 0.3555 target = 0.065811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.056404 restraints weight = 63519.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.057898 restraints weight = 31624.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.058910 restraints weight = 19387.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.059617 restraints weight = 13639.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.060128 restraints weight = 10621.960| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13008 Z= 0.158 Angle : 0.722 16.203 18822 Z= 0.408 Chirality : 0.046 0.282 2143 Planarity : 0.005 0.050 1360 Dihedral : 31.662 158.814 4077 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.01 % Allowed : 28.13 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.29), residues: 758 helix: 1.51 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.69 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 76 TYR 0.022 0.002 TYR H 80 PHE 0.019 0.002 PHE A 67 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (13008) covalent geometry : angle 0.72221 / 0.41 (18822) hydrogen bonds : bond 0.04643 / 3.14 ( 778) hydrogen bonds : angle 3.44536 / 2.57 ( 1938) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1700.36 seconds wall clock time: 30 minutes 13.96 seconds (1813.96 seconds total)