Starting phenix.real_space_refine on Wed Sep 17 23:43:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9geo_51296/09_2025/9geo_51296.cif Found real_map, /net/cci-nas-00/data/ceres_data/9geo_51296/09_2025/9geo_51296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9geo_51296/09_2025/9geo_51296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9geo_51296/09_2025/9geo_51296.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9geo_51296/09_2025/9geo_51296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9geo_51296/09_2025/9geo_51296.map" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 290 5.49 5 S 12 5.16 5 C 6598 2.51 5 N 2248 2.21 5 O 3052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12200 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Time building chain proxies: 3.56, per 1000 atoms: 0.29 Number of scatterers: 12200 At special positions: 0 Unit cell: (73.44, 114.24, 121.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 290 15.00 O 3052 8.00 N 2248 7.00 C 6598 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: 1.14 Conformation dependent library (CDL) restraints added in 498.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1418 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 72.9% alpha, 3.2% beta 137 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.779A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.542A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.527A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.800A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.691A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.510A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 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 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.751A 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: 7.079A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.763A 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: 6.961A 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: 7.052A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 411 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.56 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: 2217 1.33 - 1.45: 4170 1.45 - 1.57: 5762 1.57 - 1.69: 578 1.69 - 1.81: 22 Bond restraints: 12749 Sorted by residual: bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" C3' DC J 51 " pdb=" O3' DC J 51 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" CG PRO C 48 " pdb=" CD PRO C 48 " ideal model delta sigma weight residual 1.503 1.464 0.039 3.40e-02 8.65e+02 1.33e+00 bond pdb=" C SER C 18 " pdb=" N SER C 19 " ideal model delta sigma weight residual 1.334 1.319 0.016 1.43e-02 4.89e+03 1.21e+00 bond pdb=" CG1 ILE A 119 " pdb=" CD1 ILE A 119 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.12e+00 ... (remaining 12744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 17033 1.00 - 1.99: 1129 1.99 - 2.99: 271 2.99 - 3.99: 19 3.99 - 4.98: 9 Bond angle restraints: 18461 Sorted by residual: angle pdb=" C3' DT J -28 " pdb=" C2' DT J -28 " pdb=" C1' DT J -28 " ideal model delta sigma weight residual 101.60 98.31 3.29 1.50e+00 4.44e-01 4.81e+00 angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 123.37 -3.17 1.50e+00 4.44e-01 4.46e+00 angle pdb=" C3' DC I -25 " pdb=" C2' DC I -25 " pdb=" C1' DC I -25 " ideal model delta sigma weight residual 101.60 98.53 3.07 1.50e+00 4.44e-01 4.18e+00 angle pdb=" CB GLU H 68 " pdb=" CG GLU H 68 " pdb=" CD GLU H 68 " ideal model delta sigma weight residual 112.60 116.00 -3.40 1.70e+00 3.46e-01 4.00e+00 angle pdb=" C3' DA I -68 " pdb=" C2' DA I -68 " pdb=" C1' DA I -68 " ideal model delta sigma weight residual 101.60 98.74 2.86 1.50e+00 4.44e-01 3.63e+00 ... (remaining 18456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.83: 5375 33.83 - 67.67: 1525 67.67 - 101.50: 21 101.50 - 135.33: 1 135.33 - 169.16: 2 Dihedral angle restraints: 6924 sinusoidal: 4728 harmonic: 2196 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 50.84 169.16 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC J 51 " pdb=" C3' DC J 51 " pdb=" O3' DC J 51 " pdb=" P DG J 52 " ideal model delta sinusoidal sigma weight residual 220.00 70.41 149.59 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 91.33 128.67 1 3.50e+01 8.16e-04 1.27e+01 ... (remaining 6921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1399 0.030 - 0.061: 544 0.061 - 0.091: 111 0.091 - 0.121: 45 0.121 - 0.151: 4 Chirality restraints: 2103 Sorted by residual: chirality pdb=" CA PRO A 43 " pdb=" N PRO A 43 " pdb=" C PRO A 43 " pdb=" CB PRO A 43 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" CA ILE H 86 " pdb=" N ILE H 86 " pdb=" C ILE H 86 " pdb=" CB ILE H 86 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-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 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 2100 not shown) Planarity restraints: 1331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A 43 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " 0.025 2.00e-02 2.50e+03 1.08e-02 3.51e+00 pdb=" N9 DG I -35 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -26 " 0.022 2.00e-02 2.50e+03 1.09e-02 2.66e+00 pdb=" N1 DC I -26 " -0.020 2.00e-02 2.50e+03 pdb=" C2 DC I -26 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC I -26 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DC I -26 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I -26 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I -26 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I -26 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC I -26 " -0.005 2.00e-02 2.50e+03 ... (remaining 1328 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1131 2.74 - 3.28: 10173 3.28 - 3.82: 24214 3.82 - 4.36: 30965 4.36 - 4.90: 43278 Nonbonded interactions: 109761 Sorted by model distance: nonbonded pdb=" O HIS E 113 " pdb=" O HOH E 201 " model vdw 2.199 3.040 nonbonded pdb=" O HIS B 75 " pdb=" NH2 ARG D 89 " model vdw 2.199 3.120 nonbonded pdb=" NH2 ARG C 32 " pdb=" OE2 GLU D 32 " model vdw 2.204 3.120 nonbonded pdb=" OE2 GLU B 53 " pdb=" O HOH B 201 " model vdw 2.223 3.040 nonbonded pdb=" O LEU B 97 " pdb=" O HOH B 202 " model vdw 2.244 3.040 ... (remaining 109756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.280 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 16.480 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.005 0.043 12749 Z= 0.205 Angle : 0.566 4.983 18461 Z= 0.345 Chirality : 0.035 0.151 2103 Planarity : 0.004 0.052 1331 Dihedral : 28.684 169.163 5506 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.23 % Allowed : 20.06 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.29), residues: 740 helix: 1.92 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.11 (0.33), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 35 TYR 0.012 0.002 TYR D 34 PHE 0.008 0.002 PHE D 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00469 (12749) covalent geometry : angle 0.56553 (18461) hydrogen bonds : bond 0.11799 ( 761) hydrogen bonds : angle 3.86455 ( 1906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.305 Fit side-chains REVERT: A 115 LYS cc_start: 0.8048 (mtpm) cc_final: 0.7649 (mtmt) REVERT: A 129 ARG cc_start: 0.7656 (ttt180) cc_final: 0.6741 (tmt170) REVERT: B 91 LYS cc_start: 0.8217 (tttt) cc_final: 0.7794 (ttpt) REVERT: C 36 LYS cc_start: 0.8058 (mttt) cc_final: 0.7766 (mtmt) REVERT: C 61 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7133 (mm-30) REVERT: C 64 GLU cc_start: 0.7289 (tt0) cc_final: 0.7074 (tt0) REVERT: C 95 LYS cc_start: 0.8308 (tppt) cc_final: 0.7979 (tptp) REVERT: C 99 ARG cc_start: 0.8424 (mmt-90) cc_final: 0.7369 (mtp180) REVERT: C 104 GLN cc_start: 0.8645 (mt0) cc_final: 0.7799 (mm110) REVERT: D 109 SER cc_start: 0.8182 (t) cc_final: 0.7750 (m) REVERT: E 56 LYS cc_start: 0.8576 (tttt) cc_final: 0.8128 (ttpp) REVERT: E 59 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7726 (pt0) REVERT: E 76 GLN cc_start: 0.7134 (mt0) cc_final: 0.6654 (pt0) REVERT: E 129 ARG cc_start: 0.7932 (ttt180) cc_final: 0.6644 (tpt90) REVERT: E 131 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.6537 (mtp85) REVERT: F 93 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7736 (mm-40) REVERT: G 95 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7502 (tmtt) REVERT: G 99 ARG cc_start: 0.8107 (mmt180) cc_final: 0.7088 (mmm160) REVERT: G 104 GLN cc_start: 0.8223 (mt0) cc_final: 0.7409 (mm110) REVERT: H 31 LYS cc_start: 0.7956 (tptt) cc_final: 0.7291 (tptm) REVERT: H 113 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7703 (ttmm) outliers start: 14 outliers final: 7 residues processed: 97 average time/residue: 0.9569 time to fit residues: 97.6843 Evaluate side-chains 94 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 88 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.165488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.119297 restraints weight = 10370.733| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 0.67 r_work: 0.3050 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.0566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12749 Z= 0.190 Angle : 0.552 5.681 18461 Z= 0.337 Chirality : 0.034 0.188 2103 Planarity : 0.004 0.052 1331 Dihedral : 30.799 166.031 4032 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.55 % Allowed : 17.99 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.29), residues: 740 helix: 2.20 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -1.04 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 96 TYR 0.012 0.001 TYR B 51 PHE 0.008 0.002 PHE A 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00428 (12749) covalent geometry : angle 0.55220 (18461) hydrogen bonds : bond 0.04650 ( 761) hydrogen bonds : angle 2.95604 ( 1906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.334 Fit side-chains REVERT: A 129 ARG cc_start: 0.7864 (ttt180) cc_final: 0.7477 (tmt170) REVERT: C 99 ARG cc_start: 0.8331 (mmt-90) cc_final: 0.7791 (mtp180) REVERT: C 104 GLN cc_start: 0.8571 (mt0) cc_final: 0.7967 (mm110) REVERT: C 118 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.5748 (mptt) REVERT: D 102 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: D 109 SER cc_start: 0.8578 (t) cc_final: 0.8373 (m) REVERT: E 56 LYS cc_start: 0.8774 (tttt) cc_final: 0.8459 (ttpp) REVERT: E 76 GLN cc_start: 0.7483 (mt0) cc_final: 0.7242 (pt0) REVERT: E 129 ARG cc_start: 0.7979 (ttt180) cc_final: 0.7370 (tpt90) REVERT: G 95 LYS cc_start: 0.8309 (ttmt) cc_final: 0.8044 (tmtt) REVERT: G 99 ARG cc_start: 0.8181 (mmt180) cc_final: 0.7823 (mmm160) REVERT: G 104 GLN cc_start: 0.8343 (mt0) cc_final: 0.7843 (mm110) REVERT: H 31 LYS cc_start: 0.7933 (tptt) cc_final: 0.7461 (tptm) REVERT: H 113 LYS cc_start: 0.8497 (ttpt) cc_final: 0.8153 (ttmm) outliers start: 16 outliers final: 7 residues processed: 103 average time/residue: 0.9802 time to fit residues: 106.2385 Evaluate side-chains 97 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 98 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN G 110 ASN H 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.165067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.118659 restraints weight = 10429.132| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 0.68 r_work: 0.3039 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12749 Z= 0.196 Angle : 0.555 5.458 18461 Z= 0.338 Chirality : 0.034 0.186 2103 Planarity : 0.004 0.054 1331 Dihedral : 30.793 166.473 4015 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.03 % Allowed : 18.15 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.29), residues: 740 helix: 2.33 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.05 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.012 0.001 TYR D 34 PHE 0.008 0.002 PHE A 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00444 (12749) covalent geometry : angle 0.55481 (18461) hydrogen bonds : bond 0.04637 ( 761) hydrogen bonds : angle 2.87519 ( 1906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.317 Fit side-chains REVERT: A 129 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7472 (tmt170) REVERT: B 59 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8190 (tttt) REVERT: C 61 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7315 (mm-30) REVERT: C 99 ARG cc_start: 0.8315 (mmt-90) cc_final: 0.7774 (mtp180) REVERT: C 104 GLN cc_start: 0.8548 (mt0) cc_final: 0.7957 (mm110) REVERT: C 108 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8633 (mp) REVERT: C 118 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.5744 (mptt) REVERT: D 102 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: D 109 SER cc_start: 0.8546 (t) cc_final: 0.8344 (m) REVERT: E 56 LYS cc_start: 0.8792 (tttt) cc_final: 0.8551 (ttpp) REVERT: E 76 GLN cc_start: 0.7493 (mt0) cc_final: 0.7252 (pt0) REVERT: E 129 ARG cc_start: 0.7979 (ttt180) cc_final: 0.7371 (tpt90) REVERT: G 95 LYS cc_start: 0.8307 (ttmt) cc_final: 0.8061 (tmtt) REVERT: G 99 ARG cc_start: 0.8161 (mmt180) cc_final: 0.7838 (mmm160) REVERT: G 104 GLN cc_start: 0.8371 (mt0) cc_final: 0.7865 (mm110) REVERT: H 31 LYS cc_start: 0.7952 (tptt) cc_final: 0.7496 (tptm) REVERT: H 113 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8163 (ttmm) outliers start: 19 outliers final: 8 residues processed: 105 average time/residue: 0.9343 time to fit residues: 103.2354 Evaluate side-chains 100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 98 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN G 110 ASN H 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.164409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.117914 restraints weight = 10415.476| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 0.67 r_work: 0.3050 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12749 Z= 0.199 Angle : 0.555 5.051 18461 Z= 0.338 Chirality : 0.035 0.177 2103 Planarity : 0.004 0.053 1331 Dihedral : 30.744 165.960 4015 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.50 % Allowed : 18.95 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.29), residues: 740 helix: 2.37 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.09 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.014 0.001 TYR D 34 PHE 0.008 0.002 PHE A 67 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00452 (12749) covalent geometry : angle 0.55528 (18461) hydrogen bonds : bond 0.04662 ( 761) hydrogen bonds : angle 2.85097 ( 1906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.7864 (ttt180) cc_final: 0.7449 (tmt170) REVERT: B 59 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8194 (tttt) REVERT: C 61 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7346 (mm-30) REVERT: C 99 ARG cc_start: 0.8319 (mmt-90) cc_final: 0.7803 (mtp180) REVERT: C 104 GLN cc_start: 0.8553 (mt0) cc_final: 0.7961 (mm110) REVERT: C 108 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8628 (mp) REVERT: C 118 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.5718 (mptt) REVERT: D 102 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6716 (mp0) REVERT: D 109 SER cc_start: 0.8584 (t) cc_final: 0.8357 (m) REVERT: E 56 LYS cc_start: 0.8792 (tttt) cc_final: 0.8547 (ttpp) REVERT: E 76 GLN cc_start: 0.7506 (mt0) cc_final: 0.7250 (pt0) REVERT: E 129 ARG cc_start: 0.7974 (ttt180) cc_final: 0.7355 (tpt90) REVERT: F 92 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7614 (mtp85) REVERT: G 95 LYS cc_start: 0.8269 (ttmt) cc_final: 0.8034 (tmtt) REVERT: G 99 ARG cc_start: 0.8172 (mmt180) cc_final: 0.7841 (mmm160) REVERT: G 104 GLN cc_start: 0.8357 (mt0) cc_final: 0.7858 (mm110) REVERT: H 31 LYS cc_start: 0.7961 (tptt) cc_final: 0.7501 (tptm) REVERT: H 113 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8178 (ttmm) outliers start: 22 outliers final: 8 residues processed: 103 average time/residue: 0.9985 time to fit residues: 108.2056 Evaluate side-chains 97 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.165605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.119115 restraints weight = 10423.826| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 0.68 r_work: 0.3061 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12749 Z= 0.163 Angle : 0.543 4.969 18461 Z= 0.333 Chirality : 0.033 0.164 2103 Planarity : 0.004 0.051 1331 Dihedral : 30.730 166.002 4013 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.66 % Allowed : 18.63 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.29), residues: 740 helix: 2.45 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.04 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.012 0.001 TYR D 34 PHE 0.009 0.001 PHE A 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00354 (12749) covalent geometry : angle 0.54321 (18461) hydrogen bonds : bond 0.04436 ( 761) hydrogen bonds : angle 2.84175 ( 1906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8542 (ttt180) cc_final: 0.8221 (ttm170) REVERT: A 120 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7638 (mtt) REVERT: A 129 ARG cc_start: 0.7855 (ttt180) cc_final: 0.7433 (tmt170) REVERT: B 59 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8171 (tttt) REVERT: C 61 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: C 99 ARG cc_start: 0.8323 (mmt-90) cc_final: 0.7780 (mtp180) REVERT: C 104 GLN cc_start: 0.8571 (mt0) cc_final: 0.7970 (mm110) REVERT: C 108 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8623 (mp) REVERT: C 118 LYS cc_start: 0.6802 (OUTLIER) cc_final: 0.5694 (mptt) REVERT: D 102 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: D 109 SER cc_start: 0.8567 (t) cc_final: 0.8330 (m) REVERT: E 56 LYS cc_start: 0.8784 (tttt) cc_final: 0.8535 (ttpp) REVERT: E 76 GLN cc_start: 0.7494 (mt0) cc_final: 0.7237 (pt0) REVERT: E 129 ARG cc_start: 0.7962 (ttt180) cc_final: 0.7327 (tpt90) REVERT: F 92 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7588 (mtp85) REVERT: G 51 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7962 (tp) REVERT: G 95 LYS cc_start: 0.8274 (ttmt) cc_final: 0.8029 (tmtt) REVERT: G 99 ARG cc_start: 0.8194 (mmt180) cc_final: 0.7829 (mmm160) REVERT: G 104 GLN cc_start: 0.8358 (mt0) cc_final: 0.7847 (mm110) REVERT: H 31 LYS cc_start: 0.7950 (tptt) cc_final: 0.7474 (tptm) REVERT: H 113 LYS cc_start: 0.8505 (ttpt) cc_final: 0.8157 (ttmm) outliers start: 23 outliers final: 9 residues processed: 102 average time/residue: 1.0069 time to fit residues: 107.8188 Evaluate side-chains 102 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 64 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.165501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.119114 restraints weight = 10353.331| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 0.68 r_work: 0.3045 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12749 Z= 0.180 Angle : 0.545 4.911 18461 Z= 0.334 Chirality : 0.034 0.167 2103 Planarity : 0.004 0.051 1331 Dihedral : 30.726 166.114 4013 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.87 % Allowed : 19.59 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.41 (0.29), residues: 740 helix: 2.49 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.04 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 42 TYR 0.012 0.001 TYR D 34 PHE 0.008 0.001 PHE A 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00404 (12749) covalent geometry : angle 0.54478 (18461) hydrogen bonds : bond 0.04451 ( 761) hydrogen bonds : angle 2.83174 ( 1906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8537 (ttt180) cc_final: 0.8226 (ttm170) REVERT: A 129 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7430 (tmt170) REVERT: B 59 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8174 (tttt) REVERT: C 61 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7296 (mm-30) REVERT: C 64 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7112 (pt0) REVERT: C 99 ARG cc_start: 0.8316 (mmt-90) cc_final: 0.7787 (mtp180) REVERT: C 104 GLN cc_start: 0.8573 (mt0) cc_final: 0.7971 (mm110) REVERT: C 108 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8629 (mp) REVERT: C 118 LYS cc_start: 0.6810 (OUTLIER) cc_final: 0.5692 (mptt) REVERT: D 102 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: D 109 SER cc_start: 0.8572 (t) cc_final: 0.8340 (m) REVERT: E 56 LYS cc_start: 0.8786 (tttt) cc_final: 0.8534 (ttpp) REVERT: E 76 GLN cc_start: 0.7521 (mt0) cc_final: 0.7234 (pt0) REVERT: E 129 ARG cc_start: 0.7965 (ttt180) cc_final: 0.7338 (tpt90) REVERT: F 92 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7594 (mtp85) REVERT: G 95 LYS cc_start: 0.8280 (ttmt) cc_final: 0.8034 (tmtt) REVERT: G 99 ARG cc_start: 0.8182 (mmt180) cc_final: 0.7816 (mmm160) REVERT: G 104 GLN cc_start: 0.8363 (mt0) cc_final: 0.7845 (mm110) REVERT: H 31 LYS cc_start: 0.7957 (tptt) cc_final: 0.7482 (tptm) REVERT: H 113 LYS cc_start: 0.8508 (ttpt) cc_final: 0.8220 (ttmm) outliers start: 18 outliers final: 9 residues processed: 101 average time/residue: 0.9899 time to fit residues: 105.1318 Evaluate side-chains 101 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.164333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.120075 restraints weight = 10261.679| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 0.68 r_work: 0.3004 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12749 Z= 0.238 Angle : 0.581 5.168 18461 Z= 0.350 Chirality : 0.036 0.188 2103 Planarity : 0.005 0.054 1331 Dihedral : 30.815 166.006 4013 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.82 % Allowed : 18.63 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.29), residues: 740 helix: 2.30 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.16 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.014 0.002 TYR D 34 PHE 0.008 0.002 PHE A 67 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00551 (12749) covalent geometry : angle 0.58065 (18461) hydrogen bonds : bond 0.05136 ( 761) hydrogen bonds : angle 2.90864 ( 1906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.7853 (ttt180) cc_final: 0.7422 (tmt170) REVERT: B 59 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8150 (tttt) REVERT: C 61 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: C 64 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7154 (pt0) REVERT: C 99 ARG cc_start: 0.8352 (mmt-90) cc_final: 0.7797 (mtp180) REVERT: C 108 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8631 (mp) REVERT: C 118 LYS cc_start: 0.6826 (OUTLIER) cc_final: 0.5701 (mptt) REVERT: D 102 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: D 109 SER cc_start: 0.8562 (t) cc_final: 0.8338 (m) REVERT: E 56 LYS cc_start: 0.8803 (tttt) cc_final: 0.8542 (ttpp) REVERT: E 76 GLN cc_start: 0.7494 (mt0) cc_final: 0.7215 (pt0) REVERT: E 129 ARG cc_start: 0.8024 (ttt180) cc_final: 0.7365 (tpt90) REVERT: F 92 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7644 (mtp85) REVERT: G 95 LYS cc_start: 0.8290 (ttmt) cc_final: 0.8033 (tmtt) REVERT: G 99 ARG cc_start: 0.8216 (mmt180) cc_final: 0.7840 (mmm160) REVERT: G 104 GLN cc_start: 0.8364 (mt0) cc_final: 0.7841 (mm110) REVERT: H 31 LYS cc_start: 0.7973 (tptt) cc_final: 0.7487 (tptm) REVERT: H 113 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8165 (ttmm) outliers start: 24 outliers final: 15 residues processed: 104 average time/residue: 0.9756 time to fit residues: 106.9251 Evaluate side-chains 106 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.165778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120383 restraints weight = 10309.113| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 0.67 r_work: 0.3029 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12749 Z= 0.161 Angle : 0.553 5.065 18461 Z= 0.339 Chirality : 0.033 0.164 2103 Planarity : 0.004 0.051 1331 Dihedral : 30.806 166.034 4013 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.34 % Allowed : 18.63 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.29), residues: 740 helix: 2.46 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.09 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 42 TYR 0.012 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00345 (12749) covalent geometry : angle 0.55304 (18461) hydrogen bonds : bond 0.04569 ( 761) hydrogen bonds : angle 2.89150 ( 1906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.7784 (ttt180) cc_final: 0.7321 (tmt170) REVERT: B 59 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8098 (tttt) REVERT: C 61 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7199 (mm-30) REVERT: C 64 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6997 (pt0) REVERT: C 92 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8185 (mt-10) REVERT: C 99 ARG cc_start: 0.8303 (mmt-90) cc_final: 0.7721 (mtp180) REVERT: C 104 GLN cc_start: 0.8595 (mt0) cc_final: 0.7935 (mm110) REVERT: C 108 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8618 (mp) REVERT: C 118 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.5683 (mptt) REVERT: D 102 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: D 109 SER cc_start: 0.8476 (t) cc_final: 0.8244 (m) REVERT: E 56 LYS cc_start: 0.8756 (tttt) cc_final: 0.8481 (ttpp) REVERT: E 76 GLN cc_start: 0.7399 (mt0) cc_final: 0.7113 (pt0) REVERT: E 129 ARG cc_start: 0.7955 (ttt180) cc_final: 0.7239 (tpt90) REVERT: F 92 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7559 (mtp85) REVERT: G 95 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7956 (tmtt) REVERT: G 99 ARG cc_start: 0.8169 (mmt180) cc_final: 0.7759 (mmm160) REVERT: G 104 GLN cc_start: 0.8324 (mt0) cc_final: 0.7768 (mm110) REVERT: H 31 LYS cc_start: 0.7908 (tptt) cc_final: 0.7393 (tptm) REVERT: H 113 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8150 (ttmm) outliers start: 21 outliers final: 12 residues processed: 102 average time/residue: 0.9946 time to fit residues: 106.8992 Evaluate side-chains 104 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 68 optimal weight: 0.0870 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.161883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.115178 restraints weight = 10246.539| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 0.71 r_work: 0.2995 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 12749 Z= 0.332 Angle : 0.655 5.843 18461 Z= 0.387 Chirality : 0.042 0.219 2103 Planarity : 0.005 0.056 1331 Dihedral : 31.209 166.242 4013 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.34 % Allowed : 18.95 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.29), residues: 740 helix: 1.95 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.38 (0.34), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 42 TYR 0.017 0.002 TYR E 54 PHE 0.009 0.003 PHE H 67 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00781 (12749) covalent geometry : angle 0.65484 (18461) hydrogen bonds : bond 0.06126 ( 761) hydrogen bonds : angle 3.08765 ( 1906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.340 Fit side-chains REVERT: A 129 ARG cc_start: 0.7881 (ttt180) cc_final: 0.7471 (tmt170) REVERT: B 59 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8164 (tttt) REVERT: C 61 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: C 64 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7149 (pt0) REVERT: C 92 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8268 (mt-10) REVERT: C 99 ARG cc_start: 0.8401 (mmt-90) cc_final: 0.7814 (mtp180) REVERT: C 108 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8702 (mp) REVERT: D 102 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: D 109 SER cc_start: 0.8555 (t) cc_final: 0.8346 (m) REVERT: E 56 LYS cc_start: 0.8813 (tttt) cc_final: 0.8487 (ttpp) REVERT: E 76 GLN cc_start: 0.7519 (mt0) cc_final: 0.7247 (pt0) REVERT: E 129 ARG cc_start: 0.8040 (ttt180) cc_final: 0.7385 (tpt90) REVERT: G 51 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8054 (tp) REVERT: G 95 LYS cc_start: 0.8279 (ttmt) cc_final: 0.8015 (tmtt) REVERT: G 99 ARG cc_start: 0.8247 (mmt180) cc_final: 0.7840 (mmm160) REVERT: G 104 GLN cc_start: 0.8392 (mt0) cc_final: 0.7903 (mm110) REVERT: H 31 LYS cc_start: 0.8004 (tptt) cc_final: 0.7514 (tptm) REVERT: H 113 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8184 (ttmm) outliers start: 21 outliers final: 11 residues processed: 96 average time/residue: 1.0041 time to fit residues: 101.5707 Evaluate side-chains 94 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.165224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.121118 restraints weight = 10202.442| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.69 r_work: 0.3009 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12749 Z= 0.170 Angle : 0.580 5.050 18461 Z= 0.355 Chirality : 0.036 0.157 2103 Planarity : 0.004 0.062 1331 Dihedral : 31.150 166.902 4013 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.55 % Allowed : 19.90 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.29), residues: 740 helix: 2.23 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.21 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 42 TYR 0.013 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00373 (12749) covalent geometry : angle 0.58033 (18461) hydrogen bonds : bond 0.04771 ( 761) hydrogen bonds : angle 3.00613 ( 1906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.7825 (ttt180) cc_final: 0.7376 (tmt170) REVERT: B 59 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8127 (tttt) REVERT: C 61 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7321 (mm-30) REVERT: C 99 ARG cc_start: 0.8376 (mmt-90) cc_final: 0.7806 (mtp180) REVERT: C 104 GLN cc_start: 0.8624 (mt0) cc_final: 0.8015 (mm110) REVERT: C 108 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8654 (mp) REVERT: C 118 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.5671 (mptt) REVERT: D 102 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: D 109 SER cc_start: 0.8542 (t) cc_final: 0.8309 (m) REVERT: E 56 LYS cc_start: 0.8774 (tttt) cc_final: 0.8501 (ttpp) REVERT: E 76 GLN cc_start: 0.7473 (mt0) cc_final: 0.7187 (pt0) REVERT: E 129 ARG cc_start: 0.8001 (ttt180) cc_final: 0.7316 (tpt90) REVERT: G 95 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7978 (tmtt) REVERT: G 99 ARG cc_start: 0.8224 (mmt180) cc_final: 0.7826 (mmm160) REVERT: G 104 GLN cc_start: 0.8363 (mt0) cc_final: 0.7872 (mm110) REVERT: H 31 LYS cc_start: 0.7970 (tptt) cc_final: 0.7480 (tptm) REVERT: H 113 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8196 (ttmm) outliers start: 16 outliers final: 8 residues processed: 96 average time/residue: 1.0377 time to fit residues: 104.8071 Evaluate side-chains 94 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 110 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.164232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.117647 restraints weight = 10242.829| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 0.67 r_work: 0.3079 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12749 Z= 0.197 Angle : 0.577 4.919 18461 Z= 0.350 Chirality : 0.035 0.160 2103 Planarity : 0.004 0.062 1331 Dihedral : 31.058 166.885 4013 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.23 % Allowed : 20.38 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.29), residues: 740 helix: 2.33 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.15 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.012 0.002 TYR D 34 PHE 0.008 0.002 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00451 (12749) covalent geometry : angle 0.57727 (18461) hydrogen bonds : bond 0.04818 ( 761) hydrogen bonds : angle 2.92539 ( 1906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4023.54 seconds wall clock time: 69 minutes 13.33 seconds (4153.33 seconds total)