Starting phenix.real_space_refine on Sat Aug 23 09:52:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlb_36391/08_2025/8jlb_36391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlb_36391/08_2025/8jlb_36391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jlb_36391/08_2025/8jlb_36391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlb_36391/08_2025/8jlb_36391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jlb_36391/08_2025/8jlb_36391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlb_36391/08_2025/8jlb_36391.map" } resolution = 2.36 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= 0.005 sd= 0.050 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-2.0-5787/lib/python3.9/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: 2.43, per 1000 atoms: 0.21 Number of scatterers: 11844 At special positions: 0 Unit cell: (117.66, 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: 0.91 Conformation dependent library (CDL) restraints added in 307.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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 269 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.981A 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: 4.421A 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: 3.998A 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: 4.504A 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: 6.901A 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: 7.166A 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: 6.485A 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: 6.979A 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: 7.294A 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 269 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2141 1.33 - 1.45: 4215 1.45 - 1.57: 5692 1.57 - 1.69: 577 1.69 - 1.81: 20 Bond restraints: 12645 Sorted by residual: bond pdb=" N ARG A 129 " pdb=" CA ARG A 129 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.20e-02 6.94e+03 4.00e+00 bond pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" C3' DC I 49 " pdb=" C2' DC I 49 " ideal model delta sigma weight residual 1.525 1.547 -0.022 2.00e-02 2.50e+03 1.26e+00 bond pdb=" C ASN F 64 " pdb=" O ASN F 64 " ideal model delta sigma weight residual 1.236 1.249 -0.013 1.15e-02 7.56e+03 1.21e+00 bond pdb=" C LEU B 49 " pdb=" O LEU B 49 " ideal model delta sigma weight residual 1.235 1.250 -0.015 1.33e-02 5.65e+03 1.19e+00 ... (remaining 12640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 17693 1.81 - 3.61: 599 3.61 - 5.42: 25 5.42 - 7.22: 3 7.22 - 9.03: 1 Bond angle restraints: 18321 Sorted by residual: angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 111.34 117.97 -6.63 1.82e+00 3.02e-01 1.33e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.34 117.74 -6.40 1.82e+00 3.02e-01 1.24e+01 angle pdb=" CB MET F 84 " pdb=" CG MET F 84 " pdb=" SD MET F 84 " ideal model delta sigma weight residual 112.70 121.73 -9.03 3.00e+00 1.11e-01 9.06e+00 angle pdb=" CA ARG A 129 " pdb=" C ARG A 129 " pdb=" O ARG A 129 " ideal model delta sigma weight residual 120.90 117.88 3.02 1.07e+00 8.73e-01 7.96e+00 angle pdb=" CA MET D 59 " pdb=" CB MET D 59 " pdb=" CG MET D 59 " ideal model delta sigma weight residual 114.10 119.11 -5.01 2.00e+00 2.50e-01 6.29e+00 ... (remaining 18316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.34: 4319 21.34 - 42.68: 1358 42.68 - 64.02: 1117 64.02 - 85.37: 51 85.37 - 106.71: 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 55.63 -55.63 1 1.00e+01 1.00e-02 4.18e+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 -134.86 44.86 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG A 131 " pdb=" CD ARG A 131 " pdb=" NE ARG A 131 " pdb=" CZ ARG A 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 - 0.034: 1338 0.034 - 0.068: 498 0.068 - 0.102: 190 0.102 - 0.136: 50 0.136 - 0.171: 7 Chirality restraints: 2083 Sorted by residual: chirality pdb=" CA ARG A 129 " pdb=" N ARG A 129 " pdb=" C ARG A 129 " pdb=" CB ARG A 129 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" C3' DG I 54 " pdb=" C4' DG I 54 " pdb=" O3' DG I 54 " pdb=" C2' DG I 54 " both_signs ideal model delta sigma weight residual False -2.66 -2.81 0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 2080 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 129 " 0.903 9.50e-02 1.11e+02 4.05e-01 9.94e+01 pdb=" NE ARG A 129 " -0.054 2.00e-02 2.50e+03 pdb=" CZ ARG A 129 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 129 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 129 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 69 " -0.028 2.00e-02 2.50e+03 1.66e-02 6.19e+00 pdb=" N1 DC I 69 " 0.039 2.00e-02 2.50e+03 pdb=" C2 DC I 69 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DC I 69 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DC I 69 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 69 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 69 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC I 69 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC I 69 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.030 2.00e-02 2.50e+03 1.35e-02 5.46e+00 pdb=" N9 DG I 47 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.003 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 20 2.57 - 3.15: 8418 3.15 - 3.74: 21350 3.74 - 4.32: 30563 4.32 - 4.90: 43287 Nonbonded interactions: 103638 Sorted by model distance: nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 1.988 3.040 nonbonded pdb=" O2 DC I -23 " pdb=" N2 DG J 23 " model vdw 2.133 2.496 nonbonded pdb=" OG SER C 40 " pdb=" O SER D 87 " model vdw 2.215 3.040 nonbonded pdb=" OG SER H 36 " pdb=" ND2 ASN H 63 " model vdw 2.305 3.120 nonbonded pdb=" N GLU E 59 " pdb=" OE1 GLU E 59 " model vdw 2.382 3.120 ... (remaining 103633 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.890 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.004 0.037 12645 Z= 0.190 Angle : 0.693 9.028 18321 Z= 0.436 Chirality : 0.043 0.171 2083 Planarity : 0.012 0.405 1316 Dihedral : 29.909 106.706 5465 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.16 % Allowed : 18.34 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.28), residues: 730 helix: 0.83 (0.20), residues: 534 sheet: None (None), residues: 0 loop : -0.32 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 42 TYR 0.019 0.002 TYR F 88 PHE 0.008 0.001 PHE A 84 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00394 (12645) covalent geometry : angle 0.69315 (18321) hydrogen bonds : bond 0.07193 ( 781) hydrogen bonds : angle 3.38801 ( 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 112 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: C 84 GLN cc_start: 0.8654 (tp40) cc_final: 0.8440 (tp40) outliers start: 1 outliers final: 1 residues processed: 111 average time/residue: 0.9538 time to fit residues: 110.7536 Evaluate side-chains 102 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 95 GLN ** G 73 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 = 0.3662 r_free = 0.3662 target = 0.120742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.109781 restraints weight = 15692.002| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 0.72 r_work: 0.3418 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12645 Z= 0.166 Angle : 0.554 5.156 18321 Z= 0.345 Chirality : 0.034 0.119 2083 Planarity : 0.004 0.030 1316 Dihedral : 30.767 101.034 4005 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.81 % Allowed : 17.21 % Favored : 81.98 % 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 aren not related in a simple way. whole: 3.33 (0.31), residues: 730 helix: 2.99 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.13 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 35 TYR 0.012 0.001 TYR D 121 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00352 (12645) covalent geometry : angle 0.55447 (18321) hydrogen bonds : bond 0.04512 ( 781) hydrogen bonds : angle 2.79025 ( 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 134 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 0.299 Fit side-chains REVERT: A 120 MET cc_start: 0.8052 (mtt) cc_final: 0.7661 (mtt) REVERT: E 58 THR cc_start: 0.8619 (p) cc_final: 0.8239 (t) REVERT: E 131 ARG cc_start: 0.8304 (mtt180) cc_final: 0.7943 (mtt180) REVERT: E 133 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6791 (mp0) outliers start: 5 outliers final: 2 residues processed: 132 average time/residue: 0.7810 time to fit residues: 108.4173 Evaluate side-chains 127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain H residue 36 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 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 = 0.3661 r_free = 0.3661 target = 0.120698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.109656 restraints weight = 15780.365| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 0.72 r_work: 0.3410 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12645 Z= 0.160 Angle : 0.537 7.123 18321 Z= 0.335 Chirality : 0.033 0.127 2083 Planarity : 0.004 0.035 1316 Dihedral : 30.553 95.972 4003 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.30 % Allowed : 17.05 % Favored : 81.66 % 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 aren not related in a simple way. whole: 3.51 (0.30), residues: 730 helix: 3.12 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.05 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.011 0.001 TYR D 121 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00342 (12645) covalent geometry : angle 0.53687 (18321) hydrogen bonds : bond 0.04471 ( 781) hydrogen bonds : angle 2.68105 ( 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 136 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.328 Fit side-chains REVERT: A 65 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8350 (tp) REVERT: C 73 ASN cc_start: 0.7851 (t0) cc_final: 0.7536 (t160) REVERT: E 58 THR cc_start: 0.8673 (p) cc_final: 0.8253 (t) REVERT: E 133 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: F 93 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7855 (mm-40) REVERT: G 114 VAL cc_start: 0.8791 (p) cc_final: 0.8458 (t) outliers start: 8 outliers final: 4 residues processed: 131 average time/residue: 0.9961 time to fit residues: 136.7275 Evaluate side-chains 135 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 75 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 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 = 0.3560 r_free = 0.3560 target = 0.113242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102377 restraints weight = 15884.996| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 0.73 r_work: 0.3304 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12645 Z= 0.272 Angle : 0.618 9.033 18321 Z= 0.377 Chirality : 0.040 0.136 2083 Planarity : 0.004 0.041 1316 Dihedral : 30.299 91.558 4003 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.27 % Allowed : 16.72 % Favored : 81.01 % 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 aren not related in a simple way. whole: 2.95 (0.30), residues: 730 helix: 2.69 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.23 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 129 TYR 0.017 0.002 TYR D 121 PHE 0.010 0.002 PHE D 70 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00624 (12645) covalent geometry : angle 0.61841 (18321) hydrogen bonds : bond 0.05865 ( 781) hydrogen bonds : angle 2.89743 ( 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 129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.303 Fit side-chains REVERT: A 65 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8418 (tp) REVERT: C 91 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.4215 (tt0) REVERT: E 58 THR cc_start: 0.8723 (p) cc_final: 0.8345 (t) REVERT: E 133 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: F 93 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7950 (mm-40) REVERT: G 91 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6021 (tp30) outliers start: 14 outliers final: 6 residues processed: 124 average time/residue: 1.0158 time to fit residues: 131.6204 Evaluate side-chains 129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 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 = 0.3568 r_free = 0.3568 target = 0.113781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.102954 restraints weight = 15816.418| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 0.72 r_work: 0.3312 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12645 Z= 0.222 Angle : 0.600 10.381 18321 Z= 0.368 Chirality : 0.037 0.148 2083 Planarity : 0.004 0.040 1316 Dihedral : 30.305 91.788 4003 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.11 % Allowed : 17.05 % Favored : 80.84 % 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 aren not related in a simple way. whole: 2.96 (0.30), residues: 730 helix: 2.71 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.23 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.015 0.002 TYR D 121 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00498 (12645) covalent geometry : angle 0.59981 (18321) hydrogen bonds : bond 0.05597 ( 781) hydrogen bonds : angle 2.88431 ( 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 130 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.308 Fit side-chains REVERT: A 65 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8405 (tp) REVERT: C 91 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.4296 (tt0) REVERT: E 58 THR cc_start: 0.8708 (p) cc_final: 0.8345 (t) REVERT: E 133 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: F 93 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7937 (mm-40) REVERT: G 91 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.5992 (tp30) outliers start: 13 outliers final: 5 residues processed: 123 average time/residue: 1.0949 time to fit residues: 140.5942 Evaluate side-chains 127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 36 SER 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: 0.7980 chunk 14 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 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 = 0.3571 r_free = 0.3571 target = 0.114021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.103211 restraints weight = 15848.560| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 0.72 r_work: 0.3315 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12645 Z= 0.214 Angle : 0.586 5.403 18321 Z= 0.364 Chirality : 0.037 0.132 2083 Planarity : 0.004 0.039 1316 Dihedral : 30.298 92.295 4003 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.79 % Allowed : 17.53 % Favored : 80.68 % 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 aren not related in a simple way. whole: 3.00 (0.30), residues: 730 helix: 2.74 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.23 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 40 TYR 0.014 0.002 TYR D 121 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00481 (12645) covalent geometry : angle 0.58565 (18321) hydrogen bonds : bond 0.05481 ( 781) hydrogen bonds : angle 2.85370 ( 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 129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.184 Fit side-chains REVERT: A 65 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8397 (tp) REVERT: C 91 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.4303 (tt0) REVERT: E 58 THR cc_start: 0.8704 (p) cc_final: 0.8341 (t) REVERT: E 133 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: F 93 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7935 (mm-40) REVERT: G 91 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.5971 (tp30) outliers start: 11 outliers final: 5 residues processed: 124 average time/residue: 1.0785 time to fit residues: 139.4496 Evaluate side-chains 128 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 97 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 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 = 0.3582 r_free = 0.3582 target = 0.114828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.104047 restraints weight = 15764.035| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 0.72 r_work: 0.3329 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 12645 Z= 0.173 Angle : 0.575 5.406 18321 Z= 0.357 Chirality : 0.035 0.129 2083 Planarity : 0.004 0.038 1316 Dihedral : 30.317 92.505 4003 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.62 % Allowed : 18.18 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.14 (0.30), residues: 730 helix: 2.84 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.012 0.002 TYR D 121 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00368 (12645) covalent geometry : angle 0.57451 (18321) hydrogen bonds : bond 0.05191 ( 781) hydrogen bonds : angle 2.82884 ( 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 130 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.323 Fit side-chains REVERT: A 65 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8379 (tp) REVERT: C 36 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8365 (mtpp) REVERT: C 91 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.4356 (tt0) REVERT: E 58 THR cc_start: 0.8698 (p) cc_final: 0.8338 (t) REVERT: E 133 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: F 93 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7922 (mm-40) REVERT: G 91 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6194 (tp30) outliers start: 10 outliers final: 4 residues processed: 126 average time/residue: 1.0489 time to fit residues: 138.2218 Evaluate side-chains 129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 78 SER 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: 6.9990 chunk 3 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 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 = 0.3585 r_free = 0.3585 target = 0.115036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.104266 restraints weight = 15883.283| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 0.72 r_work: 0.3333 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12645 Z= 0.208 Angle : 0.572 5.445 18321 Z= 0.354 Chirality : 0.036 0.132 2083 Planarity : 0.004 0.039 1316 Dihedral : 30.207 91.367 4003 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.27 % Allowed : 17.69 % 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 aren not related in a simple way. whole: 3.11 (0.30), residues: 730 helix: 2.82 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.18 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.013 0.002 TYR D 121 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00464 (12645) covalent geometry : angle 0.57173 (18321) hydrogen bonds : bond 0.05124 ( 781) hydrogen bonds : angle 2.76453 ( 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 132 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.308 Fit side-chains REVERT: C 36 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8351 (mtpp) REVERT: C 91 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.4378 (tt0) REVERT: E 58 THR cc_start: 0.8686 (p) cc_final: 0.8349 (t) REVERT: E 133 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: G 91 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6336 (tp30) outliers start: 14 outliers final: 7 residues processed: 126 average time/residue: 1.1178 time to fit residues: 147.1951 Evaluate side-chains 130 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 36 SER 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: 1.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 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 = 0.3589 r_free = 0.3589 target = 0.115304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104583 restraints weight = 15682.480| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 0.71 r_work: 0.3338 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12645 Z= 0.188 Angle : 0.570 6.396 18321 Z= 0.353 Chirality : 0.035 0.130 2083 Planarity : 0.004 0.039 1316 Dihedral : 30.204 91.343 4003 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.79 % Allowed : 18.34 % Favored : 79.87 % 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 aren not related in a simple way. whole: 3.15 (0.30), residues: 730 helix: 2.84 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.15 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.014 0.002 TYR D 121 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00414 (12645) covalent geometry : angle 0.57010 (18321) hydrogen bonds : bond 0.05029 ( 781) hydrogen bonds : angle 2.77015 ( 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 130 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.323 Fit side-chains REVERT: C 36 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8346 (mtpp) REVERT: C 91 GLU cc_start: 0.6748 (OUTLIER) cc_final: 0.4374 (tt0) REVERT: E 58 THR cc_start: 0.8684 (p) cc_final: 0.8349 (t) REVERT: E 133 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: G 91 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6321 (tp30) outliers start: 11 outliers final: 6 residues processed: 125 average time/residue: 1.1015 time to fit residues: 144.0865 Evaluate side-chains 128 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 36 SER 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: 1.9990 chunk 21 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 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 = 0.3591 r_free = 0.3591 target = 0.115476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104735 restraints weight = 15873.673| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 0.72 r_work: 0.3341 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12645 Z= 0.179 Angle : 0.566 6.543 18321 Z= 0.352 Chirality : 0.035 0.129 2083 Planarity : 0.004 0.038 1316 Dihedral : 30.204 91.329 4003 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.46 % Allowed : 18.51 % 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 aren not related in a simple way. whole: 3.18 (0.30), residues: 730 helix: 2.87 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.14 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.013 0.002 TYR D 121 PHE 0.009 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00388 (12645) covalent geometry : angle 0.56639 (18321) hydrogen bonds : bond 0.04990 ( 781) hydrogen bonds : angle 2.76747 ( 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 127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.225 Fit side-chains REVERT: C 36 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8348 (mtpp) REVERT: C 91 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.4374 (tt0) REVERT: E 58 THR cc_start: 0.8684 (p) cc_final: 0.8347 (t) REVERT: E 133 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: G 91 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6377 (tp30) outliers start: 9 outliers final: 5 residues processed: 124 average time/residue: 1.0039 time to fit residues: 130.1275 Evaluate side-chains 127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 36 SER 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: 4.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 59 optimal weight: 0.0470 chunk 37 optimal weight: 0.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 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 = 0.3590 r_free = 0.3590 target = 0.115358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104618 restraints weight = 15802.168| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 0.72 r_work: 0.3339 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12645 Z= 0.198 Angle : 0.570 6.569 18321 Z= 0.353 Chirality : 0.036 0.130 2083 Planarity : 0.004 0.039 1316 Dihedral : 30.184 90.938 4003 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.62 % Allowed : 18.34 % 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 aren not related in a simple way. whole: 3.15 (0.30), residues: 730 helix: 2.84 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.15 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.013 0.002 TYR D 121 PHE 0.008 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00437 (12645) covalent geometry : angle 0.57001 (18321) hydrogen bonds : bond 0.05023 ( 781) hydrogen bonds : angle 2.76869 ( 1948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4298.71 seconds wall clock time: 73 minutes 37.43 seconds (4417.43 seconds total)