Starting phenix.real_space_refine on Wed Aug 5 19:00:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jld_36393/08_2026/8jld_36393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jld_36393/08_2026/8jld_36393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jld_36393/08_2026/8jld_36393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jld_36393/08_2026/8jld_36393.map" model { file = "/net/cci-nas-00/data/ceres_data/8jld_36393/08_2026/8jld_36393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jld_36393/08_2026/8jld_36393.cif" } resolution = 2.48 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= 0.006 sd= 0.049 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 289 5.49 5 S 10 5.16 5 C 6540 2.51 5 N 2221 2.21 5 O 2784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11844 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 782 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 782 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.61, per 1000 atoms: 0.22 Number of scatterers: 11844 At special positions: 0 Unit cell: (118.72, 110.24, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 289 15.00 O 2784 8.00 N 2221 7.00 C 6540 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: 0.97 Conformation dependent library (CDL) restraints added in 224.3 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 74.0% alpha, 3.2% beta 144 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.005A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.452A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.063A 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 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing 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 73 removed outlier: 4.475A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.051A 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 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.181A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.492A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.042A 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: 7.240A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 414 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2608 1.34 - 1.46: 4027 1.46 - 1.58: 5413 1.58 - 1.70: 577 1.70 - 1.82: 20 Bond restraints: 12645 Sorted by residual: bond pdb=" C3' DC I 49 " pdb=" C2' DC I 49 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.53e+01 bond pdb=" C3' DG I -53 " pdb=" C2' DG I -53 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.44e+01 bond pdb=" C3' DG J -22 " pdb=" C2' DG J -22 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C5' DA I 50 " pdb=" C4' DA I 50 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.20e+01 bond pdb=" C3' DC I -62 " pdb=" C2' DC I -62 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 ... (remaining 12640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 16635 1.54 - 3.09: 1543 3.09 - 4.63: 127 4.63 - 6.17: 10 6.17 - 7.72: 6 Bond angle restraints: 18321 Sorted by residual: angle pdb=" O4' DA J 16 " pdb=" C1' DA J 16 " pdb=" N9 DA J 16 " ideal model delta sigma weight residual 108.00 112.05 -4.05 7.00e-01 2.04e+00 3.35e+01 angle pdb=" O5' DA I 50 " pdb=" C5' DA I 50 " pdb=" C4' DA I 50 " ideal model delta sigma weight residual 109.40 113.86 -4.46 8.00e-01 1.56e+00 3.10e+01 angle pdb=" O5' DA I -45 " pdb=" C5' DA I -45 " pdb=" C4' DA I -45 " ideal model delta sigma weight residual 109.40 113.68 -4.28 8.00e-01 1.56e+00 2.86e+01 angle pdb=" O4' DA I -45 " pdb=" C4' DA I -45 " pdb=" C3' DA I -45 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.47e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 18316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 4330 21.29 - 42.58: 1362 42.58 - 63.88: 1107 63.88 - 85.17: 46 85.17 - 106.46: 4 Dihedral angle restraints: 6849 sinusoidal: 4697 harmonic: 2152 Sorted by residual: dihedral pdb=" CD ARG A 129 " pdb=" NE ARG A 129 " pdb=" CZ ARG A 129 " pdb=" NH1 ARG A 129 " ideal model delta sinusoidal sigma weight residual 0.00 60.23 -60.23 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CG ARG C 71 " pdb=" CD ARG C 71 " pdb=" NE ARG C 71 " pdb=" CZ ARG C 71 " ideal model delta sinusoidal sigma weight residual 90.00 42.05 47.95 2 1.50e+01 4.44e-03 1.18e+01 dihedral pdb=" CG ARG E 131 " pdb=" CD ARG E 131 " pdb=" NE ARG E 131 " pdb=" CZ ARG E 131 " ideal model delta sinusoidal sigma weight residual -90.00 -134.79 44.79 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 6846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1191 0.033 - 0.067: 617 0.067 - 0.100: 227 0.100 - 0.133: 39 0.133 - 0.166: 9 Chirality restraints: 2083 Sorted by residual: chirality pdb=" CA GLU G 64 " pdb=" N GLU G 64 " pdb=" C GLU G 64 " pdb=" CB GLU G 64 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA ARG E 63 " pdb=" N ARG E 63 " pdb=" C ARG E 63 " pdb=" CB ARG E 63 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 2080 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 129 " 0.946 9.50e-02 1.11e+02 4.24e-01 1.09e+02 pdb=" NE ARG A 129 " -0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 129 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 129 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 129 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 95 " 0.422 9.50e-02 1.11e+02 1.89e-01 2.19e+01 pdb=" NE ARG B 95 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 95 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 95 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 95 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 19 " 0.016 2.00e-02 2.50e+03 1.71e-02 6.58e+00 pdb=" N1 DC J 19 " -0.039 2.00e-02 2.50e+03 pdb=" C2 DC J 19 " 0.028 2.00e-02 2.50e+03 pdb=" O2 DC J 19 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC J 19 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC J 19 " 0.000 2.00e-02 2.50e+03 pdb=" N4 DC J 19 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC J 19 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC J 19 " 0.004 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 19 2.53 - 3.12: 7925 3.12 - 3.72: 20865 3.72 - 4.31: 30867 4.31 - 4.90: 43915 Nonbonded interactions: 103591 Sorted by model distance: nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 1.941 3.040 nonbonded pdb=" O2 DC I -23 " pdb=" N2 DG J 23 " model vdw 2.114 2.496 nonbonded pdb=" NH1 ARG C 11 " pdb=" O2 DT I -42 " model vdw 2.217 3.120 nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 71 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR G 39 " pdb=" OE2 GLU H 71 " model vdw 2.297 3.040 ... (remaining 103586 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.720 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 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 : 0.006 0.036 12645 Z= 0.534 Angle : 0.868 7.717 18321 Z= 0.762 Chirality : 0.043 0.166 2083 Planarity : 0.014 0.424 1316 Dihedral : 29.740 106.461 5465 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.32 % Allowed : 17.37 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.27), residues: 730 helix: 0.79 (0.20), residues: 538 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 131 TYR 0.011 0.002 TYR F 51 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.53 (12645) covalent geometry : angle 0.86824 / 0.76 (18321) hydrogen bonds : bond 0.07192 / 4.74 ( 781) hydrogen bonds : angle 3.35582 / 2.53 ( 1948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 0.300 Fit side-chains REVERT: G 73 ASN cc_start: 0.8425 (t0) cc_final: 0.8170 (t0) outliers start: 2 outliers final: 1 residues processed: 163 average time/residue: 0.9557 time to fit residues: 163.5995 Evaluate side-chains 151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN E 68 GLN F 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.103706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.090525 restraints weight = 18253.443| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 0.97 r_work: 0.3186 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12645 Z= 0.140 Angle : 0.660 7.065 18321 Z= 0.382 Chirality : 0.049 0.237 2083 Planarity : 0.005 0.057 1316 Dihedral : 31.742 105.105 4005 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.11 % Allowed : 18.34 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.31), residues: 730 helix: 2.89 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.10 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 40 TYR 0.007 0.001 TYR D 83 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.14 (12645) covalent geometry : angle 0.65979 / 0.38 (18321) hydrogen bonds : bond 0.05277 / 3.61 ( 781) hydrogen bonds : angle 2.92767 / 2.21 ( 1948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.308 Fit side-chains REVERT: A 129 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7718 (tpt90) REVERT: C 11 ARG cc_start: 0.8113 (pmm-80) cc_final: 0.7830 (mtm180) REVERT: C 13 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8555 (mmmt) REVERT: C 73 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.8032 (t160) REVERT: D 76 GLU cc_start: 0.8331 (tp30) cc_final: 0.8105 (tp30) REVERT: D 79 ARG cc_start: 0.8721 (ttp-170) cc_final: 0.8516 (ttp-170) REVERT: F 84 MET cc_start: 0.8799 (mmm) cc_final: 0.8546 (mmp) REVERT: F 92 ARG cc_start: 0.9001 (ptm-80) cc_final: 0.8780 (ptm-80) REVERT: G 73 ASN cc_start: 0.8392 (t0) cc_final: 0.8123 (t0) outliers start: 13 outliers final: 7 residues processed: 168 average time/residue: 0.9104 time to fit residues: 160.7937 Evaluate side-chains 171 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 18 optimal weight: 0.0980 chunk 85 optimal weight: 10.9990 chunk 28 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN D 95 GLN F 27 GLN F 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.103189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.090131 restraints weight = 18451.791| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 0.98 r_work: 0.3186 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12645 Z= 0.141 Angle : 0.611 6.016 18321 Z= 0.363 Chirality : 0.046 0.215 2083 Planarity : 0.004 0.033 1316 Dihedral : 31.367 108.797 4003 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.11 % Allowed : 17.86 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.64 (0.31), residues: 730 helix: 3.20 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.00 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.018 0.001 TYR D 83 PHE 0.009 0.001 PHE E 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 (12645) covalent geometry : angle 0.61124 / 0.36 (18321) hydrogen bonds : bond 0.04946 / 3.37 ( 781) hydrogen bonds : angle 2.77098 / 2.10 ( 1948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.317 Fit side-chains REVERT: B 35 ARG cc_start: 0.8581 (mtp85) cc_final: 0.8302 (mtp85) REVERT: B 93 GLN cc_start: 0.8391 (mt0) cc_final: 0.8076 (mp10) REVERT: C 13 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8573 (mmmt) REVERT: C 73 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8046 (t160) REVERT: C 77 ARG cc_start: 0.9113 (mtm-85) cc_final: 0.8880 (mtt90) REVERT: D 76 GLU cc_start: 0.8377 (tp30) cc_final: 0.8084 (tp30) REVERT: D 79 ARG cc_start: 0.8744 (ttp-170) cc_final: 0.8461 (ttp-170) REVERT: E 53 ARG cc_start: 0.8687 (tmm-80) cc_final: 0.8476 (ttt-90) REVERT: E 129 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7918 (ttp80) REVERT: F 92 ARG cc_start: 0.8993 (ptm-80) cc_final: 0.8786 (ptm-80) REVERT: G 73 ASN cc_start: 0.8397 (t0) cc_final: 0.8096 (t0) REVERT: G 91 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6367 (mm-30) outliers start: 13 outliers final: 7 residues processed: 173 average time/residue: 0.9462 time to fit residues: 172.1673 Evaluate side-chains 176 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 75 optimal weight: 10.0000 chunk 77 optimal weight: 10.9990 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 44 optimal weight: 0.0270 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 overall best weight: 2.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 76 GLN F 27 GLN F 93 GLN H 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.099119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.086135 restraints weight = 18428.143| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 0.97 r_work: 0.3113 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12645 Z= 0.209 Angle : 0.678 7.436 18321 Z= 0.385 Chirality : 0.050 0.229 2083 Planarity : 0.004 0.037 1316 Dihedral : 31.269 110.665 4003 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.08 % Allowed : 18.18 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.30), residues: 730 helix: 2.94 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.11 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 72 TYR 0.016 0.002 TYR H 121 PHE 0.009 0.002 PHE A 67 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 (12645) covalent geometry : angle 0.67755 / 0.38 (18321) hydrogen bonds : bond 0.05681 / 3.84 ( 781) hydrogen bonds : angle 2.89046 / 2.18 ( 1948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8313 (mmm160) cc_final: 0.7812 (tpt90) REVERT: B 35 ARG cc_start: 0.8624 (mtp85) cc_final: 0.8312 (mtp85) REVERT: C 11 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.8100 (pmm-80) REVERT: C 73 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8161 (t160) REVERT: C 77 ARG cc_start: 0.9110 (mtm-85) cc_final: 0.8832 (mtt90) REVERT: E 83 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7815 (mtm180) REVERT: E 129 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8000 (ttp80) REVERT: F 92 ARG cc_start: 0.9026 (ptm-80) cc_final: 0.8797 (ptm-80) REVERT: F 93 GLN cc_start: 0.8495 (mt0) cc_final: 0.8234 (mt0) REVERT: G 73 ASN cc_start: 0.8463 (t0) cc_final: 0.8163 (t0) REVERT: G 91 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.3607 (tp30) outliers start: 19 outliers final: 7 residues processed: 171 average time/residue: 0.9332 time to fit residues: 167.7690 Evaluate side-chains 175 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.099908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.086908 restraints weight = 18323.930| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 0.97 r_work: 0.3128 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12645 Z= 0.142 Angle : 0.654 9.091 18321 Z= 0.374 Chirality : 0.048 0.227 2083 Planarity : 0.004 0.034 1316 Dihedral : 31.272 111.349 4003 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.92 % Allowed : 18.34 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.40 (0.30), residues: 730 helix: 3.02 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.07 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 35 TYR 0.011 0.002 TYR D 83 PHE 0.009 0.001 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 (12645) covalent geometry : angle 0.65380 / 0.37 (18321) hydrogen bonds : bond 0.05386 / 3.65 ( 781) hydrogen bonds : angle 2.84762 / 2.15 ( 1948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8301 (mmm160) cc_final: 0.7813 (tpt90) REVERT: B 35 ARG cc_start: 0.8605 (mtp85) cc_final: 0.8295 (mtp85) REVERT: C 11 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.8049 (pmm-80) REVERT: C 73 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8136 (t160) REVERT: C 77 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8844 (mtt90) REVERT: C 99 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7731 (mtm110) REVERT: E 129 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7951 (ttp80) REVERT: F 92 ARG cc_start: 0.9018 (ptm-80) cc_final: 0.8781 (ptm-80) REVERT: F 93 GLN cc_start: 0.8460 (mt0) cc_final: 0.8227 (mt0) REVERT: G 73 ASN cc_start: 0.8442 (t0) cc_final: 0.8153 (t0) REVERT: G 91 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.3592 (tp30) outliers start: 18 outliers final: 8 residues processed: 172 average time/residue: 0.8436 time to fit residues: 152.7124 Evaluate side-chains 175 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 0.0370 chunk 88 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.099927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.086945 restraints weight = 18372.104| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 0.97 r_work: 0.3128 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12645 Z= 0.159 Angle : 0.647 6.979 18321 Z= 0.372 Chirality : 0.048 0.222 2083 Planarity : 0.004 0.050 1316 Dihedral : 31.249 111.751 4003 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.60 % Allowed : 19.64 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.40 (0.30), residues: 730 helix: 3.03 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.06 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.015 0.001 TYR D 83 PHE 0.009 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (12645) covalent geometry : angle 0.64669 / 0.37 (18321) hydrogen bonds : bond 0.05348 / 3.64 ( 781) hydrogen bonds : angle 2.81518 / 2.13 ( 1948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8305 (mmm160) cc_final: 0.7814 (tpt90) REVERT: B 35 ARG cc_start: 0.8609 (mtp85) cc_final: 0.8324 (mtp85) REVERT: C 11 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8055 (pmm-80) REVERT: C 73 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8147 (t160) REVERT: C 77 ARG cc_start: 0.9106 (mtm-85) cc_final: 0.8860 (mtt90) REVERT: C 99 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7751 (mtm110) REVERT: E 129 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7973 (ttp80) REVERT: F 92 ARG cc_start: 0.9016 (ptm-80) cc_final: 0.8775 (ptm-80) REVERT: F 93 GLN cc_start: 0.8474 (mt0) cc_final: 0.8246 (mt0) REVERT: G 73 ASN cc_start: 0.8451 (t0) cc_final: 0.8155 (t0) REVERT: G 91 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.3570 (tp30) outliers start: 16 outliers final: 8 residues processed: 169 average time/residue: 0.9321 time to fit residues: 165.6406 Evaluate side-chains 177 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 38 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.100291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.087319 restraints weight = 18283.219| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 0.97 r_work: 0.3135 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12645 Z= 0.139 Angle : 0.643 9.080 18321 Z= 0.370 Chirality : 0.047 0.220 2083 Planarity : 0.004 0.083 1316 Dihedral : 31.243 112.273 4003 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.92 % Allowed : 19.16 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.46 (0.30), residues: 730 helix: 3.07 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.04 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.016 0.001 TYR D 83 PHE 0.009 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.14 (12645) covalent geometry : angle 0.64251 / 0.37 (18321) hydrogen bonds : bond 0.05248 / 3.57 ( 781) hydrogen bonds : angle 2.80307 / 2.12 ( 1948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8289 (mmm160) cc_final: 0.7810 (tpt90) REVERT: B 35 ARG cc_start: 0.8603 (mtp85) cc_final: 0.8314 (mtp85) REVERT: B 93 GLN cc_start: 0.8380 (mt0) cc_final: 0.7990 (mm-40) REVERT: C 11 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7989 (pmm-80) REVERT: C 73 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8133 (t160) REVERT: C 77 ARG cc_start: 0.9101 (mtm-85) cc_final: 0.8866 (mtt90) REVERT: C 99 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7757 (mtm110) REVERT: E 129 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7960 (ttp80) REVERT: F 92 ARG cc_start: 0.9006 (ptm-80) cc_final: 0.8764 (ptm-80) REVERT: F 93 GLN cc_start: 0.8455 (mt0) cc_final: 0.8231 (mt0) REVERT: G 73 ASN cc_start: 0.8435 (t0) cc_final: 0.8139 (t0) REVERT: G 91 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.3555 (tp30) outliers start: 18 outliers final: 8 residues processed: 172 average time/residue: 0.8944 time to fit residues: 161.7353 Evaluate side-chains 177 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 43 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.099303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.086418 restraints weight = 18398.601| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.97 r_work: 0.3119 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12645 Z= 0.174 Angle : 0.647 6.591 18321 Z= 0.373 Chirality : 0.048 0.244 2083 Planarity : 0.004 0.032 1316 Dihedral : 31.078 116.087 4003 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.25 % Allowed : 19.32 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.32 (0.30), residues: 730 helix: 2.95 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.03 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 79 TYR 0.016 0.002 TYR D 83 PHE 0.012 0.002 PHE A 67 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (12645) covalent geometry : angle 0.64692 / 0.37 (18321) hydrogen bonds : bond 0.05424 / 3.68 ( 781) hydrogen bonds : angle 2.80806 / 2.12 ( 1948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8606 (mtp85) cc_final: 0.8314 (mtp85) REVERT: B 93 GLN cc_start: 0.8430 (mt0) cc_final: 0.8155 (mp10) REVERT: C 73 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8179 (t160) REVERT: C 77 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8873 (mtt90) REVERT: C 91 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.3789 (tp30) REVERT: C 99 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7748 (mtm110) REVERT: F 92 ARG cc_start: 0.9005 (ptm-80) cc_final: 0.8764 (ptm-80) REVERT: G 73 ASN cc_start: 0.8472 (t0) cc_final: 0.8163 (t0) REVERT: G 91 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.3575 (tp30) outliers start: 20 outliers final: 6 residues processed: 171 average time/residue: 0.8576 time to fit residues: 154.3433 Evaluate side-chains 172 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 76 GLN F 27 GLN F 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.099732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.086860 restraints weight = 18163.894| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 0.97 r_work: 0.3127 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12645 Z= 0.154 Angle : 0.648 7.342 18321 Z= 0.371 Chirality : 0.047 0.242 2083 Planarity : 0.004 0.032 1316 Dihedral : 31.084 116.411 4003 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.44 % Allowed : 19.64 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.36 (0.30), residues: 730 helix: 2.98 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.03 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 63 TYR 0.024 0.002 TYR D 83 PHE 0.010 0.001 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (12645) covalent geometry : angle 0.64773 / 0.37 (18321) hydrogen bonds : bond 0.05310 / 3.62 ( 781) hydrogen bonds : angle 2.79414 / 2.11 ( 1948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8214 (m-30) cc_final: 0.8004 (m-30) REVERT: A 129 ARG cc_start: 0.8275 (mmm160) cc_final: 0.7815 (tpt90) REVERT: B 35 ARG cc_start: 0.8603 (mtp85) cc_final: 0.8309 (mtp85) REVERT: B 93 GLN cc_start: 0.8410 (mt0) cc_final: 0.8022 (mm-40) REVERT: C 11 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7772 (pmm-80) REVERT: C 73 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8184 (t160) REVERT: C 77 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8876 (mtt90) REVERT: C 91 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.3608 (tp30) REVERT: C 99 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7744 (mtm110) REVERT: F 92 ARG cc_start: 0.9000 (ptm-80) cc_final: 0.8748 (ptm-80) REVERT: G 73 ASN cc_start: 0.8453 (t0) cc_final: 0.8147 (t0) REVERT: G 91 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.3551 (tp30) outliers start: 15 outliers final: 8 residues processed: 168 average time/residue: 0.7971 time to fit residues: 140.7385 Evaluate side-chains 174 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 76 GLN F 27 GLN F 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.099838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.086957 restraints weight = 18397.443| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 0.97 r_work: 0.3129 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12645 Z= 0.155 Angle : 0.647 10.816 18321 Z= 0.370 Chirality : 0.047 0.244 2083 Planarity : 0.004 0.032 1316 Dihedral : 31.066 116.986 4003 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.60 % Allowed : 20.13 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.37 (0.30), residues: 730 helix: 3.00 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.05 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 63 TYR 0.029 0.002 TYR D 83 PHE 0.010 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 (12645) covalent geometry : angle 0.64709 / 0.37 (18321) hydrogen bonds : bond 0.05264 / 3.59 ( 781) hydrogen bonds : angle 2.77512 / 2.10 ( 1948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8213 (m-30) cc_final: 0.8003 (m-30) REVERT: A 129 ARG cc_start: 0.8271 (mmm160) cc_final: 0.7815 (tpt90) REVERT: B 35 ARG cc_start: 0.8604 (mtp85) cc_final: 0.8312 (mtp85) REVERT: B 93 GLN cc_start: 0.8404 (mt0) cc_final: 0.7992 (mm-40) REVERT: C 11 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7761 (pmm-80) REVERT: C 73 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8150 (t160) REVERT: C 77 ARG cc_start: 0.9102 (mtm-85) cc_final: 0.8878 (mtt90) REVERT: C 91 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.3587 (tp30) REVERT: C 99 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7734 (mtm110) REVERT: F 84 MET cc_start: 0.8743 (mmm) cc_final: 0.8483 (mmm) REVERT: F 92 ARG cc_start: 0.8993 (ptm-80) cc_final: 0.8740 (ptm-80) REVERT: G 73 ASN cc_start: 0.8446 (t0) cc_final: 0.8139 (t0) REVERT: G 91 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.3542 (tp30) outliers start: 16 outliers final: 9 residues processed: 172 average time/residue: 0.8934 time to fit residues: 161.4964 Evaluate side-chains 177 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 52 optimal weight: 0.0170 chunk 69 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN F 27 GLN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.100036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.087194 restraints weight = 18273.908| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 0.97 r_work: 0.3136 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12645 Z= 0.141 Angle : 0.637 6.324 18321 Z= 0.368 Chirality : 0.047 0.243 2083 Planarity : 0.004 0.031 1316 Dihedral : 31.061 117.164 4003 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.44 % Allowed : 20.13 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.40 (0.30), residues: 730 helix: 3.02 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.03 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 63 TYR 0.029 0.002 TYR D 83 PHE 0.010 0.001 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 (12645) covalent geometry : angle 0.63737 / 0.37 (18321) hydrogen bonds : bond 0.05200 / 3.55 ( 781) hydrogen bonds : angle 2.76785 / 2.09 ( 1948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4531.65 seconds wall clock time: 77 minutes 32.24 seconds (4652.24 seconds total)