Starting phenix.real_space_refine on Wed May 14 02:47:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlb_36391/05_2025/8jlb_36391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlb_36391/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jlb_36391/05_2025/8jlb_36391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlb_36391/05_2025/8jlb_36391.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlb_36391/05_2025/8jlb_36391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlb_36391/05_2025/8jlb_36391.cif" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.01, per 1000 atoms: 0.59 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: 3.13 Conformation dependent library (CDL) restraints added in 922.7 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 269 stacking pairs defined. Time for finding SS restraints: 5.80 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: 4.70 Time building geometry restraints manager: 3.66 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: 0.380 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.090 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.004 0.001 HIS H 49 PHE 0.008 0.001 PHE A 84 TYR 0.019 0.002 TYR F 88 ARG 0.007 0.001 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.07193 ( 781) hydrogen bonds : angle 3.38801 ( 1948) covalent geometry : bond 0.00394 (12645) covalent geometry : angle 0.69315 (18321) *********************** 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 : 0.815 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 111 average time/residue: 2.1836 time to fit residues: 253.5541 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 : 0.838 ------------------------------------------------------------------------------- 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 82 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.112211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.101211 restraints weight = 15644.539| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 0.74 r_work: 0.3286 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 12645 Z= 0.320 Angle : 0.672 5.838 18321 Z= 0.407 Chirality : 0.044 0.133 2083 Planarity : 0.005 0.037 1316 Dihedral : 30.635 98.773 4005 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.62 % Allowed : 15.91 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.30), residues: 730 helix: 2.40 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 49 PHE 0.012 0.002 PHE D 70 TYR 0.022 0.003 TYR D 121 ARG 0.006 0.001 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.06348 ( 781) hydrogen bonds : angle 3.11675 ( 1948) covalent geometry : bond 0.00740 (12645) covalent geometry : angle 0.67218 (18321) *********************** 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 126 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8629 (mt) cc_final: 0.8401 (tp) REVERT: C 91 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.4322 (tt0) REVERT: E 58 THR cc_start: 0.8696 (p) cc_final: 0.8272 (t) REVERT: E 133 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: G 91 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6256 (tp30) outliers start: 10 outliers final: 3 residues processed: 124 average time/residue: 2.0670 time to fit residues: 268.9280 Evaluate side-chains 122 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 36 SER Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 52 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.114256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103416 restraints weight = 15802.717| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 0.72 r_work: 0.3320 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12645 Z= 0.184 Angle : 0.615 12.800 18321 Z= 0.378 Chirality : 0.037 0.130 2083 Planarity : 0.004 0.037 1316 Dihedral : 30.676 99.709 4003 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.27 % Allowed : 16.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.30), residues: 730 helix: 2.60 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.40 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 49 PHE 0.008 0.001 PHE E 67 TYR 0.015 0.002 TYR D 121 ARG 0.005 0.000 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.05536 ( 781) hydrogen bonds : angle 2.98909 ( 1948) covalent geometry : bond 0.00401 (12645) covalent geometry : angle 0.61490 (18321) *********************** 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 135 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8606 (mt) cc_final: 0.8383 (tp) REVERT: C 91 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.3962 (tp30) REVERT: E 58 THR cc_start: 0.8688 (p) cc_final: 0.8265 (t) REVERT: E 133 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6819 (mp0) outliers start: 14 outliers final: 5 residues processed: 128 average time/residue: 2.0709 time to fit residues: 277.6985 Evaluate side-chains 125 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 133 GLU 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 47 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.110492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.099793 restraints weight = 15921.535| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 0.74 r_work: 0.3266 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 12645 Z= 0.355 Angle : 0.674 6.003 18321 Z= 0.407 Chirality : 0.046 0.158 2083 Planarity : 0.005 0.044 1316 Dihedral : 30.383 87.218 4003 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.27 % Allowed : 16.56 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.30), residues: 730 helix: 2.28 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.46 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 49 PHE 0.012 0.002 PHE D 70 TYR 0.017 0.003 TYR D 121 ARG 0.006 0.001 ARG F 40 Details of bonding type rmsd hydrogen bonds : bond 0.06589 ( 781) hydrogen bonds : angle 3.05003 ( 1948) covalent geometry : bond 0.00825 (12645) covalent geometry : angle 0.67415 (18321) *********************** 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 128 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8345 (mtpp) REVERT: C 91 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.4183 (tt0) REVERT: E 58 THR cc_start: 0.8736 (p) cc_final: 0.8348 (t) REVERT: E 133 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: F 93 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8087 (mm-40) REVERT: G 91 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.5582 (tp30) outliers start: 14 outliers final: 5 residues processed: 124 average time/residue: 2.1486 time to fit residues: 279.3926 Evaluate side-chains 123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 78 SER 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 78 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 72 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.112407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.101719 restraints weight = 15788.026| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 0.72 r_work: 0.3295 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12645 Z= 0.194 Angle : 0.630 12.936 18321 Z= 0.385 Chirality : 0.037 0.132 2083 Planarity : 0.004 0.038 1316 Dihedral : 30.439 89.214 4003 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.27 % Allowed : 18.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.30), residues: 730 helix: 2.51 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.38 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.013 0.002 TYR D 40 ARG 0.006 0.000 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.05807 ( 781) hydrogen bonds : angle 2.97950 ( 1948) covalent geometry : bond 0.00416 (12645) covalent geometry : angle 0.63008 (18321) *********************** 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 129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8376 (tp) REVERT: C 36 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8348 (mtpp) REVERT: C 91 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.4245 (tt0) REVERT: E 58 THR cc_start: 0.8716 (p) cc_final: 0.8336 (t) REVERT: E 133 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: F 93 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7964 (mm-40) REVERT: G 91 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.5175 (tp30) outliers start: 14 outliers final: 4 residues processed: 124 average time/residue: 2.0326 time to fit residues: 264.5611 Evaluate side-chains 126 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 C residue 108 LEU 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 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 78 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.112868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.102198 restraints weight = 15896.244| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 0.72 r_work: 0.3303 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1905 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= 0.189 Angle : 0.599 5.257 18321 Z= 0.373 Chirality : 0.037 0.129 2083 Planarity : 0.004 0.038 1316 Dihedral : 30.393 90.622 4003 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.11 % Allowed : 18.67 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.30), residues: 730 helix: 2.63 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.38 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.012 0.002 TYR D 121 ARG 0.006 0.000 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.05525 ( 781) hydrogen bonds : angle 2.89781 ( 1948) covalent geometry : bond 0.00411 (12645) covalent geometry : angle 0.59854 (18321) *********************** 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 130 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8360 (mtpp) REVERT: E 58 THR cc_start: 0.8717 (p) cc_final: 0.8340 (t) REVERT: E 133 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: F 93 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.8017 (mm-40) REVERT: G 91 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.5170 (tp30) outliers start: 13 outliers final: 7 residues processed: 125 average time/residue: 2.0133 time to fit residues: 263.9065 Evaluate side-chains 127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 108 LEU Chi-restraints excluded: chain D residue 78 SER 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 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 9 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 73 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.113617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.102958 restraints weight = 15886.825| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 0.72 r_work: 0.3315 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12645 Z= 0.173 Angle : 0.592 6.404 18321 Z= 0.367 Chirality : 0.036 0.187 2083 Planarity : 0.004 0.037 1316 Dihedral : 30.387 91.240 4003 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.11 % Allowed : 18.83 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.30), residues: 730 helix: 2.73 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.35 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.012 0.002 TYR D 40 ARG 0.003 0.000 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.05274 ( 781) hydrogen bonds : angle 2.85956 ( 1948) covalent geometry : bond 0.00367 (12645) covalent geometry : angle 0.59154 (18321) *********************** 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 137 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8353 (mtpp) REVERT: C 91 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.4225 (tt0) REVERT: E 58 THR cc_start: 0.8710 (p) cc_final: 0.8334 (t) REVERT: E 131 ARG cc_start: 0.8422 (mtt180) cc_final: 0.8190 (mtt180) REVERT: E 133 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: F 93 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7939 (mm-40) REVERT: G 91 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.5396 (tp30) outliers start: 13 outliers final: 9 residues processed: 131 average time/residue: 2.1096 time to fit residues: 289.4761 Evaluate side-chains 136 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 91 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 56 LYS 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 34 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.114169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103501 restraints weight = 15877.045| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 0.72 r_work: 0.3323 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12645 Z= 0.185 Angle : 0.581 5.297 18321 Z= 0.360 Chirality : 0.035 0.130 2083 Planarity : 0.004 0.038 1316 Dihedral : 30.291 91.206 4003 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.11 % Allowed : 18.99 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.30), residues: 730 helix: 2.83 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.31 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.011 0.002 TYR D 40 ARG 0.003 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.05219 ( 781) hydrogen bonds : angle 2.79662 ( 1948) covalent geometry : bond 0.00404 (12645) covalent geometry : angle 0.58067 (18321) *********************** 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: 13 poor density : 119 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8357 (mtpp) REVERT: C 91 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.4319 (tt0) REVERT: E 58 THR cc_start: 0.8700 (p) cc_final: 0.8334 (t) REVERT: E 133 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: G 91 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.5662 (tp30) outliers start: 13 outliers final: 8 residues processed: 126 average time/residue: 1.9883 time to fit residues: 263.0023 Evaluate side-chains 131 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 56 LYS 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 8 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.114778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.104122 restraints weight = 15872.541| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 0.72 r_work: 0.3332 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12645 Z= 0.164 Angle : 0.572 6.605 18321 Z= 0.356 Chirality : 0.035 0.140 2083 Planarity : 0.004 0.037 1316 Dihedral : 30.302 90.989 4003 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.95 % Allowed : 19.16 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.31), residues: 730 helix: 2.84 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.29 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE E 67 TYR 0.012 0.001 TYR D 40 ARG 0.003 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.04978 ( 781) hydrogen bonds : angle 2.79819 ( 1948) covalent geometry : bond 0.00349 (12645) covalent geometry : angle 0.57214 (18321) *********************** 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 135 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8356 (mtpp) REVERT: C 91 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.4302 (tt0) REVERT: E 58 THR cc_start: 0.8695 (p) cc_final: 0.8335 (t) REVERT: E 133 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: G 91 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.5436 (tp30) outliers start: 12 outliers final: 7 residues processed: 131 average time/residue: 2.0072 time to fit residues: 276.1301 Evaluate side-chains 135 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 91 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER 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 78 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.116410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.105701 restraints weight = 15790.250| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 0.72 r_work: 0.3355 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1989 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= 0.173 Angle : 0.555 5.315 18321 Z= 0.346 Chirality : 0.034 0.128 2083 Planarity : 0.004 0.038 1316 Dihedral : 30.119 89.297 4003 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.30 % Allowed : 20.29 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.30), residues: 730 helix: 2.96 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.26 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.012 0.001 TYR D 40 ARG 0.004 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.04677 ( 781) hydrogen bonds : angle 2.72468 ( 1948) covalent geometry : bond 0.00376 (12645) covalent geometry : angle 0.55538 (18321) ********************** 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 132 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8095 (mtt) cc_final: 0.7688 (mtt) REVERT: C 36 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8361 (mtpp) REVERT: C 91 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.4327 (tt0) REVERT: D 59 MET cc_start: 0.8649 (mmt) cc_final: 0.8419 (tpt) REVERT: E 58 THR cc_start: 0.8682 (p) cc_final: 0.8321 (t) REVERT: E 133 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: G 17 ARG cc_start: 0.8610 (mtp180) cc_final: 0.8334 (mtp180) outliers start: 8 outliers final: 5 residues processed: 129 average time/residue: 2.2133 time to fit residues: 299.0719 Evaluate side-chains 129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 C residue 108 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain E residue 133 GLU 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 16 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.116528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.105817 restraints weight = 15824.491| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 0.72 r_work: 0.3356 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2036 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= 0.175 Angle : 0.553 5.546 18321 Z= 0.344 Chirality : 0.034 0.128 2083 Planarity : 0.004 0.038 1316 Dihedral : 30.038 88.748 4003 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.11 % Allowed : 19.81 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.30), residues: 730 helix: 2.97 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.16 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.007 0.001 PHE E 67 TYR 0.010 0.001 TYR H 83 ARG 0.004 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 781) hydrogen bonds : angle 2.71411 ( 1948) covalent geometry : bond 0.00380 (12645) covalent geometry : angle 0.55295 (18321) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8544.90 seconds wall clock time: 147 minutes 14.29 seconds (8834.29 seconds total)