Starting phenix.real_space_refine on Tue Jul 29 11:12:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlb_36391/07_2025/8jlb_36391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlb_36391/07_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_36391/07_2025/8jlb_36391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlb_36391/07_2025/8jlb_36391.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlb_36391/07_2025/8jlb_36391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlb_36391/07_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-5711/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: 6.69, per 1000 atoms: 0.56 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: 2.75 Conformation dependent library (CDL) restraints added in 896.3 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 74.0% alpha, 3.2% beta 144 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 5.78 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: 4.57 Time building geometry restraints manager: 3.33 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: 0.520 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 32.120 Find NCS groups from input model: 0.270 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:14.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.710 ------------------------------------------------------------------------------- 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 : 0.903 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 111 average time/residue: 2.2307 time to fit residues: 259.0959 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 : 0.796 ------------------------------------------------------------------------------- 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 = 0.101212 restraints weight = 15644.541| |-----------------------------------------------------------------------------| 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: 0.3179 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 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 : 0.826 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8628 (mt) cc_final: 0.8399 (tp) REVERT: C 91 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.4323 (tt0) REVERT: E 58 THR cc_start: 0.8695 (p) cc_final: 0.8272 (t) REVERT: E 133 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: G 91 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6257 (tp30) outliers start: 10 outliers final: 3 residues processed: 124 average time/residue: 2.0774 time to fit residues: 270.2146 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 : 0.824 ------------------------------------------------------------------------------- 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: 0.8980 chunk 84 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.114332 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 = 15808.165| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 0.72 r_work: 0.3321 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1518 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= 0.182 Angle : 0.615 12.891 18321 Z= 0.378 Chirality : 0.037 0.130 2083 Planarity : 0.004 0.037 1316 Dihedral : 30.678 99.743 4003 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.88 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: 2.61 (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 0.001 TYR D 121 ARG 0.005 0.000 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.05519 ( 781) hydrogen bonds : angle 2.98793 ( 1948) covalent geometry : bond 0.00397 (12645) covalent geometry : angle 0.61455 (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 : 0.862 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8604 (mt) cc_final: 0.8383 (tp) REVERT: C 91 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.3961 (tp30) REVERT: E 58 THR cc_start: 0.8689 (p) cc_final: 0.8266 (t) REVERT: E 133 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.6815 (mp0) outliers start: 14 outliers final: 5 residues processed: 128 average time/residue: 2.0955 time to fit residues: 281.3117 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 : 0.896 ------------------------------------------------------------------------------- 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: 6.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.110475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.099801 restraints weight = 15931.441| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 0.74 r_work: 0.3265 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: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 12645 Z= 0.354 Angle : 0.676 5.969 18321 Z= 0.408 Chirality : 0.045 0.149 2083 Planarity : 0.005 0.045 1316 Dihedral : 30.356 86.741 4003 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: 2.37 (0.30), residues: 730 helix: 2.28 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.45 (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 0.002 TYR D 121 ARG 0.005 0.001 ARG F 40 Details of bonding type rmsd hydrogen bonds : bond 0.06613 ( 781) hydrogen bonds : angle 3.04503 ( 1948) covalent geometry : bond 0.00825 (12645) covalent geometry : angle 0.67571 (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 : 0.867 Fit side-chains revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8348 (mtpp) REVERT: C 91 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.4195 (tt0) REVERT: E 58 THR cc_start: 0.8737 (p) cc_final: 0.8344 (t) REVERT: E 133 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: F 93 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8037 (mm-40) REVERT: G 91 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.5403 (tp30) outliers start: 14 outliers final: 6 residues processed: 123 average time/residue: 2.5287 time to fit residues: 326.3697 Evaluate side-chains 123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.112612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101968 restraints weight = 15800.888| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 0.71 r_work: 0.3301 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1963 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= 0.189 Angle : 0.612 11.422 18321 Z= 0.378 Chirality : 0.037 0.137 2083 Planarity : 0.004 0.039 1316 Dihedral : 30.388 89.642 4003 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.11 % Allowed : 17.86 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 : -0.41 (0.38), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE D 70 TYR 0.014 0.002 TYR D 121 ARG 0.004 0.001 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.05674 ( 781) hydrogen bonds : angle 2.93952 ( 1948) covalent geometry : bond 0.00415 (12645) covalent geometry : angle 0.61221 (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 126 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8362 (mtpp) REVERT: E 58 THR cc_start: 0.8716 (p) cc_final: 0.8335 (t) REVERT: E 133 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: F 93 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7959 (mm-40) REVERT: G 91 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.5226 (tp30) outliers start: 13 outliers final: 6 residues processed: 121 average time/residue: 2.0757 time to fit residues: 263.5793 Evaluate side-chains 124 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.112627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101942 restraints weight = 15909.447| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 0.72 r_work: 0.3300 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12645 Z= 0.229 Angle : 0.604 5.429 18321 Z= 0.373 Chirality : 0.038 0.143 2083 Planarity : 0.004 0.040 1316 Dihedral : 30.309 90.525 4003 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.44 % Allowed : 17.69 % 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 (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: 2.73 (0.30), residues: 730 helix: 2.56 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.42 (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 0.013 0.002 TYR D 121 ARG 0.004 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.05640 ( 781) hydrogen bonds : angle 2.87626 ( 1948) covalent geometry : bond 0.00519 (12645) covalent geometry : angle 0.60391 (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 131 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 57 SER cc_start: 0.8191 (OUTLIER) cc_final: 0.7987 (t) REVERT: C 36 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8356 (mtpp) REVERT: C 91 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.4284 (tt0) REVERT: E 58 THR cc_start: 0.8706 (p) cc_final: 0.8343 (t) REVERT: E 133 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: G 91 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.5517 (tp30) outliers start: 15 outliers final: 8 residues processed: 126 average time/residue: 2.1784 time to fit residues: 288.1716 Evaluate side-chains 129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER 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 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 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: 5.9990 chunk 10 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102645 restraints weight = 15894.310| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 0.72 r_work: 0.3309 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12645 Z= 0.182 Angle : 0.595 11.145 18321 Z= 0.368 Chirality : 0.036 0.130 2083 Planarity : 0.004 0.040 1316 Dihedral : 30.324 90.976 4003 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: 2.86 (0.30), residues: 730 helix: 2.66 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.39 (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 0.010 0.001 TYR D 40 ARG 0.002 0.000 ARG H 72 Details of bonding type rmsd hydrogen bonds : bond 0.05341 ( 781) hydrogen bonds : angle 2.86016 ( 1948) covalent geometry : bond 0.00395 (12645) covalent geometry : angle 0.59540 (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 133 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8333 (tp) REVERT: C 36 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8359 (mtpp) REVERT: C 91 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.4229 (tt0) REVERT: E 58 THR cc_start: 0.8704 (p) cc_final: 0.8342 (t) REVERT: E 133 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: G 91 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.5229 (tp30) outliers start: 13 outliers final: 6 residues processed: 128 average time/residue: 2.0468 time to fit residues: 274.9027 Evaluate side-chains 134 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 93 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 88 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.114578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.103962 restraints weight = 15866.814| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 0.72 r_work: 0.3329 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1966 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= 0.165 Angle : 0.573 5.671 18321 Z= 0.357 Chirality : 0.035 0.130 2083 Planarity : 0.004 0.038 1316 Dihedral : 30.284 91.091 4003 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.95 % Allowed : 19.48 % Favored : 78.57 % 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: 3.02 (0.30), residues: 730 helix: 2.79 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.32 (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 0.011 0.001 TYR D 40 ARG 0.005 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.05026 ( 781) hydrogen bonds : angle 2.79032 ( 1948) covalent geometry : bond 0.00348 (12645) covalent geometry : angle 0.57264 (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 135 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8359 (mtpp) REVERT: C 91 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.4276 (tt0) REVERT: E 58 THR cc_start: 0.8702 (p) cc_final: 0.8343 (t) REVERT: E 133 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: G 91 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.5423 (tp30) outliers start: 12 outliers final: 6 residues processed: 132 average time/residue: 2.5122 time to fit residues: 347.7602 Evaluate side-chains 131 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 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 78 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.115327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104707 restraints weight = 15897.805| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 0.72 r_work: 0.3340 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12645 Z= 0.164 Angle : 0.569 7.387 18321 Z= 0.354 Chirality : 0.035 0.127 2083 Planarity : 0.004 0.038 1316 Dihedral : 30.238 90.653 4003 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.79 % Allowed : 19.81 % 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: 3.16 (0.31), residues: 730 helix: 2.89 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.28 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 31 PHE 0.008 0.001 PHE E 67 TYR 0.011 0.001 TYR F 88 ARG 0.003 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.04888 ( 781) hydrogen bonds : angle 2.76222 ( 1948) covalent geometry : bond 0.00348 (12645) covalent geometry : angle 0.56904 (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 134 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8355 (mtpp) REVERT: C 91 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.4321 (tt0) REVERT: E 58 THR cc_start: 0.8694 (p) cc_final: 0.8342 (t) REVERT: E 133 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: G 91 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.5884 (tp30) outliers start: 11 outliers final: 8 residues processed: 130 average time/residue: 2.7685 time to fit residues: 379.1933 Evaluate side-chains 134 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.116075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.105368 restraints weight = 15805.624| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 0.72 r_work: 0.3350 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12645 Z= 0.176 Angle : 0.558 6.217 18321 Z= 0.347 Chirality : 0.035 0.126 2083 Planarity : 0.004 0.054 1316 Dihedral : 30.069 88.967 4003 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.62 % Allowed : 20.13 % Favored : 78.25 % 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: 3.30 (0.31), residues: 730 helix: 2.99 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.24 (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 0.011 0.001 TYR D 40 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04696 ( 781) hydrogen bonds : angle 2.73515 ( 1948) covalent geometry : bond 0.00383 (12645) covalent geometry : angle 0.55835 (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 131 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8103 (mtt) cc_final: 0.7703 (mtt) REVERT: C 36 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8369 (mtpp) REVERT: C 91 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.4331 (tt0) REVERT: D 62 MET cc_start: 0.8883 (mmm) cc_final: 0.8631 (mmm) REVERT: E 58 THR cc_start: 0.8695 (p) cc_final: 0.8339 (t) REVERT: E 133 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: G 91 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.5858 (tp30) outliers start: 10 outliers final: 7 residues processed: 128 average time/residue: 2.1751 time to fit residues: 291.8192 Evaluate side-chains 131 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 0.0470 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.116239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.105535 restraints weight = 15824.965| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 0.72 r_work: 0.3352 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2074 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= 0.172 Angle : 0.558 6.002 18321 Z= 0.346 Chirality : 0.035 0.160 2083 Planarity : 0.004 0.039 1316 Dihedral : 30.062 88.974 4003 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.79 % Allowed : 19.97 % Favored : 78.25 % 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: 3.30 (0.30), residues: 730 helix: 2.98 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.20 (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 0.013 0.001 TYR F 88 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04664 ( 781) hydrogen bonds : angle 2.72456 ( 1948) covalent geometry : bond 0.00373 (12645) covalent geometry : angle 0.55798 (18321) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10254.77 seconds wall clock time: 184 minutes 54.18 seconds (11094.18 seconds total)