Starting phenix.real_space_refine on Wed Sep 17 04:53:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yc0_39128/09_2025/8yc0_39128.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yc0_39128/09_2025/8yc0_39128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yc0_39128/09_2025/8yc0_39128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yc0_39128/09_2025/8yc0_39128.map" model { file = "/net/cci-nas-00/data/ceres_data/8yc0_39128/09_2025/8yc0_39128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yc0_39128/09_2025/8yc0_39128.cif" } resolution = 4.12 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= -0.001 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 3009 2.51 5 N 731 2.21 5 O 858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s 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: 4635 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 203 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "b" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 218 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "d" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "f" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 933 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "g" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 907 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "m" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 268 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "n" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.47, per 1000 atoms: 0.32 Number of scatterers: 4635 At special positions: 0 Unit cell: (100.004, 86.96, 89.134, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 858 8.00 N 731 7.00 C 3009 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.04 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.04 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS f 119 " - pdb=" SG CYS f 122 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 185.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1084 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 40.0% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'a' and resid 26 through 50 removed outlier: 4.043A pdb=" N LYS a 30 " --> pdb=" O LEU a 26 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU a 31 " --> pdb=" O LEU a 27 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR a 33 " --> pdb=" O PRO a 29 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU a 34 " --> pdb=" O LYS a 30 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU a 35 " --> pdb=" O LEU a 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 54 Processing helix chain 'd' and resid 100 through 124 removed outlier: 3.620A pdb=" N VAL d 104 " --> pdb=" O ASP d 100 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA d 105 " --> pdb=" O PRO d 101 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLY d 106 " --> pdb=" O ALA d 102 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 152 removed outlier: 3.538A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 154 removed outlier: 3.517A pdb=" N ASN f 154 " --> pdb=" O TYR f 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 80 removed outlier: 3.921A pdb=" N ASP g 80 " --> pdb=" O ASN g 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 137 removed outlier: 3.694A pdb=" N SER g 116 " --> pdb=" O ALA g 112 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY g 117 " --> pdb=" O ALA g 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 257 through 289 removed outlier: 3.582A pdb=" N MET m 261 " --> pdb=" O GLU m 257 " (cutoff:3.500A) Processing helix chain 'n' and resid 253 through 288 Processing sheet with id=AA1, first strand: chain 'd' and resid 32 through 35 removed outlier: 7.525A pdb=" N VAL d 33 " --> pdb=" O LEU d 60 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU d 60 " --> pdb=" O VAL d 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 41 through 46 removed outlier: 3.843A pdb=" N VAL d 44 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE d 70 " --> pdb=" O VAL d 44 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY d 46 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARG d 68 " --> pdb=" O GLY d 46 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLN d 87 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ARG e 115 " --> pdb=" O GLN d 87 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N HIS d 89 " --> pdb=" O ARG e 115 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N PHE e 110 " --> pdb=" O CYS e 98 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N CYS e 98 " --> pdb=" O PHE e 110 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL e 97 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR e 99 " --> pdb=" O LEU e 58 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU e 58 " --> pdb=" O TYR e 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 41 removed outlier: 3.705A pdb=" N LYS e 37 " --> pdb=" O THR e 48 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY e 76 " --> pdb=" O SER e 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'f' and resid 37 through 38 removed outlier: 4.006A pdb=" N LYS f 37 " --> pdb=" O THR f 48 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR f 48 " --> pdb=" O LYS f 37 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU f 82 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 112 through 115 removed outlier: 5.591A pdb=" N TYR f 113 " --> pdb=" O TYR g 100 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY g 83 " --> pdb=" O VAL g 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'g' and resid 31 through 34 removed outlier: 3.960A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY g 75 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU g 44 " --> pdb=" O ASN g 73 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN g 73 " --> pdb=" O LEU g 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'g' and resid 54 through 57 removed outlier: 6.318A pdb=" N TRP g 55 " --> pdb=" O ILE g 62 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE g 62 " --> pdb=" O TRP g 55 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.52 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1433 1.34 - 1.47: 1125 1.47 - 1.59: 2115 1.59 - 1.71: 0 1.71 - 1.83: 51 Bond restraints: 4724 Sorted by residual: bond pdb=" C ASP a 28 " pdb=" N PRO a 29 " ideal model delta sigma weight residual 1.333 1.364 -0.031 1.44e-02 4.82e+03 4.62e+00 bond pdb=" CA ASP e 63 " pdb=" CB ASP e 63 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.69e-02 3.50e+03 1.55e+00 bond pdb=" CB PRO f 100 " pdb=" CG PRO f 100 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.46e+00 bond pdb=" N ASN e 121 " pdb=" CA ASN e 121 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.17e+00 bond pdb=" CB ASP f 137 " pdb=" CG ASP f 137 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 ... (remaining 4719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 6304 2.57 - 5.14: 80 5.14 - 7.71: 14 7.71 - 10.28: 4 10.28 - 12.85: 2 Bond angle restraints: 6404 Sorted by residual: angle pdb=" C LEU a 27 " pdb=" CA LEU a 27 " pdb=" CB LEU a 27 " ideal model delta sigma weight residual 115.89 109.41 6.48 1.32e+00 5.74e-01 2.41e+01 angle pdb=" CA CYS f 49 " pdb=" CB CYS f 49 " pdb=" SG CYS f 49 " ideal model delta sigma weight residual 114.40 123.14 -8.74 2.30e+00 1.89e-01 1.44e+01 angle pdb=" CA LEU f 114 " pdb=" CB LEU f 114 " pdb=" CG LEU f 114 " ideal model delta sigma weight residual 116.30 129.15 -12.85 3.50e+00 8.16e-02 1.35e+01 angle pdb=" N GLY d 46 " pdb=" CA GLY d 46 " pdb=" C GLY d 46 " ideal model delta sigma weight residual 111.56 115.25 -3.69 1.01e+00 9.80e-01 1.33e+01 angle pdb=" CB MET m 262 " pdb=" CG MET m 262 " pdb=" SD MET m 262 " ideal model delta sigma weight residual 112.70 123.09 -10.39 3.00e+00 1.11e-01 1.20e+01 ... (remaining 6399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 2343 16.69 - 33.39: 390 33.39 - 50.08: 118 50.08 - 66.78: 20 66.78 - 83.47: 6 Dihedral angle restraints: 2877 sinusoidal: 1184 harmonic: 1693 Sorted by residual: dihedral pdb=" CB CYS d 37 " pdb=" SG CYS d 37 " pdb=" SG CYS d 73 " pdb=" CB CYS d 73 " ideal model delta sinusoidal sigma weight residual 93.00 175.13 -82.13 1 1.00e+01 1.00e-02 8.28e+01 dihedral pdb=" CB CYS e 49 " pdb=" SG CYS e 49 " pdb=" SG CYS e 98 " pdb=" CB CYS e 98 " ideal model delta sinusoidal sigma weight residual -86.00 -15.84 -70.16 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual -86.00 -154.55 68.55 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 2874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 504 0.037 - 0.074: 174 0.074 - 0.111: 55 0.111 - 0.148: 16 0.148 - 0.186: 2 Chirality restraints: 751 Sorted by residual: chirality pdb=" CA ASP e 63 " pdb=" N ASP e 63 " pdb=" C ASP e 63 " pdb=" CB ASP e 63 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.61e-01 chirality pdb=" CA ILE d 70 " pdb=" N ILE d 70 " pdb=" C ILE d 70 " pdb=" CB ILE d 70 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ASN e 121 " pdb=" N ASN e 121 " pdb=" C ASN e 121 " pdb=" CB ASN e 121 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 748 not shown) Planarity restraints: 785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR f 99 " 0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO f 100 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO f 100 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO f 100 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR e 99 " 0.037 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO e 100 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO e 100 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO e 100 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS f 104 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.53e+00 pdb=" N PRO f 105 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO f 105 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO f 105 " 0.017 5.00e-02 4.00e+02 ... (remaining 782 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 95 2.67 - 3.23: 4543 3.23 - 3.79: 7049 3.79 - 4.34: 8421 4.34 - 4.90: 13883 Nonbonded interactions: 33991 Sorted by model distance: nonbonded pdb=" OD1 ASP e 126 " pdb=" N VAL e 127 " model vdw 2.114 3.120 nonbonded pdb=" O GLN e 92 " pdb=" OH TYR e 96 " model vdw 2.225 3.040 nonbonded pdb=" N GLU f 56 " pdb=" OE1 GLU f 56 " model vdw 2.255 3.120 nonbonded pdb=" NE2 GLN e 60 " pdb=" OD1 ASN e 65 " model vdw 2.258 3.120 nonbonded pdb=" O ILE d 24 " pdb=" OH TYR e 95 " model vdw 2.279 3.040 ... (remaining 33986 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 28 through 50) selection = (chain 'b' and resid 28 through 50) } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 153)) selection = (chain 'f' and resid 33 through 153) } 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 group one per residue 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: 0.560 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.540 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 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 0.060 4733 Z= 0.161 Angle : 0.781 12.853 6422 Z= 0.392 Chirality : 0.043 0.186 751 Planarity : 0.005 0.086 785 Dihedral : 17.513 83.473 1766 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.58 % Allowed : 39.73 % Favored : 59.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.34), residues: 565 helix: 2.06 (0.33), residues: 212 sheet: -1.22 (0.64), residues: 74 loop : -2.81 (0.30), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 63 TYR 0.016 0.001 TYR b 42 PHE 0.020 0.001 PHE g 118 TRP 0.016 0.001 TRP d 43 HIS 0.004 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4724) covalent geometry : angle 0.77359 ( 6404) SS BOND : bond 0.00354 ( 9) SS BOND : angle 2.20836 ( 18) hydrogen bonds : bond 0.17723 ( 223) hydrogen bonds : angle 6.27538 ( 648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 71 TYR cc_start: 0.7273 (m-80) cc_final: 0.6835 (m-10) REVERT: d 90 TYR cc_start: 0.7388 (m-80) cc_final: 0.6902 (m-80) REVERT: e 36 TYR cc_start: 0.6981 (m-80) cc_final: 0.5299 (m-10) REVERT: e 46 ILE cc_start: 0.8085 (mp) cc_final: 0.7839 (mm) REVERT: e 47 LEU cc_start: 0.8296 (mt) cc_final: 0.8084 (tt) REVERT: e 49 CYS cc_start: 0.6913 (t) cc_final: 0.5596 (t) REVERT: e 85 LYS cc_start: 0.7718 (mptt) cc_final: 0.7517 (mptt) REVERT: e 91 GLU cc_start: 0.8234 (tp30) cc_final: 0.8019 (tm-30) REVERT: e 92 GLN cc_start: 0.7710 (tt0) cc_final: 0.7193 (tt0) REVERT: e 117 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7622 (ttt180) REVERT: e 120 GLU cc_start: 0.8013 (pp20) cc_final: 0.7719 (pp20) REVERT: e 123 MET cc_start: 0.5173 (mtt) cc_final: 0.4751 (ptp) REVERT: g 38 GLU cc_start: 0.8295 (pm20) cc_final: 0.8070 (pm20) REVERT: g 43 LEU cc_start: 0.7667 (mt) cc_final: 0.7448 (mt) REVERT: g 80 ASP cc_start: 0.8028 (m-30) cc_final: 0.7779 (t0) REVERT: g 111 ASN cc_start: 0.7321 (m110) cc_final: 0.6744 (p0) REVERT: m 286 LYS cc_start: 0.7448 (tppt) cc_final: 0.7238 (tptt) outliers start: 3 outliers final: 0 residues processed: 154 average time/residue: 0.0909 time to fit residues: 16.9797 Evaluate side-chains 136 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 0.0070 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 ASN n 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.186879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.161542 restraints weight = 8845.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.161681 restraints weight = 12455.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.163027 restraints weight = 9830.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.163396 restraints weight = 7504.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.165031 restraints weight = 6779.186| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4733 Z= 0.158 Angle : 0.694 5.979 6422 Z= 0.363 Chirality : 0.044 0.171 751 Planarity : 0.005 0.058 785 Dihedral : 5.069 50.844 692 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.19 % Allowed : 3.68 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.34), residues: 565 helix: 2.13 (0.33), residues: 215 sheet: -1.31 (0.64), residues: 75 loop : -2.95 (0.30), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG e 101 TYR 0.010 0.002 TYR e 95 PHE 0.020 0.002 PHE b 40 TRP 0.006 0.001 TRP e 59 HIS 0.007 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 4724) covalent geometry : angle 0.68611 ( 6404) SS BOND : bond 0.00439 ( 9) SS BOND : angle 2.12553 ( 18) hydrogen bonds : bond 0.04878 ( 223) hydrogen bonds : angle 4.56380 ( 648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 36 TYR cc_start: 0.8066 (m-80) cc_final: 0.6873 (m-10) REVERT: f 101 ARG cc_start: 0.7966 (mtp85) cc_final: 0.7756 (mtp85) REVERT: f 110 PHE cc_start: 0.8167 (p90) cc_final: 0.7886 (p90) REVERT: g 39 ASP cc_start: 0.8353 (p0) cc_final: 0.7950 (p0) REVERT: g 80 ASP cc_start: 0.8329 (m-30) cc_final: 0.8036 (t0) REVERT: g 95 LYS cc_start: 0.8357 (mtpt) cc_final: 0.8035 (mtpp) REVERT: m 286 LYS cc_start: 0.8616 (tppt) cc_final: 0.8379 (tptt) REVERT: n 259 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7767 (t0) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.0849 time to fit residues: 17.3936 Evaluate side-chains 138 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 0.0980 chunk 45 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 89 HIS e 92 GLN g 86 GLN n 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.181385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.158918 restraints weight = 7650.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.159499 restraints weight = 6603.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.160295 restraints weight = 5915.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.160561 restraints weight = 5451.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.160565 restraints weight = 5158.201| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4733 Z= 0.140 Angle : 0.650 6.338 6422 Z= 0.338 Chirality : 0.043 0.186 751 Planarity : 0.005 0.056 785 Dihedral : 4.970 50.166 692 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.34), residues: 565 helix: 2.28 (0.33), residues: 217 sheet: -1.22 (0.66), residues: 71 loop : -2.93 (0.29), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG g 102 TYR 0.012 0.001 TYR g 34 PHE 0.033 0.001 PHE b 40 TRP 0.006 0.001 TRP d 43 HIS 0.005 0.001 HIS d 89 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4724) covalent geometry : angle 0.64226 ( 6404) SS BOND : bond 0.00416 ( 9) SS BOND : angle 2.03402 ( 18) hydrogen bonds : bond 0.04509 ( 223) hydrogen bonds : angle 4.23094 ( 648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 36 TYR cc_start: 0.7880 (m-80) cc_final: 0.6520 (m-80) REVERT: e 49 CYS cc_start: 0.6454 (t) cc_final: 0.5982 (t) REVERT: e 98 CYS cc_start: 0.3211 (p) cc_final: 0.2940 (p) REVERT: f 110 PHE cc_start: 0.8177 (p90) cc_final: 0.7952 (p90) REVERT: f 115 ARG cc_start: 0.8268 (ttt-90) cc_final: 0.7991 (tpt-90) REVERT: f 125 MET cc_start: 0.8460 (ppp) cc_final: 0.8179 (ppp) REVERT: g 39 ASP cc_start: 0.8168 (p0) cc_final: 0.7759 (p0) REVERT: g 80 ASP cc_start: 0.8234 (m-30) cc_final: 0.7970 (t0) REVERT: g 95 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7880 (mtpp) REVERT: m 258 LYS cc_start: 0.8430 (tppt) cc_final: 0.8218 (mmtp) REVERT: m 286 LYS cc_start: 0.8552 (tppt) cc_final: 0.8217 (tptt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.0800 time to fit residues: 15.5486 Evaluate side-chains 130 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.0570 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 0.0670 chunk 49 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.180714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.158815 restraints weight = 7724.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.159639 restraints weight = 6540.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.160063 restraints weight = 5804.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.160833 restraints weight = 5318.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.160833 restraints weight = 4872.928| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4733 Z= 0.133 Angle : 0.643 6.322 6422 Z= 0.337 Chirality : 0.043 0.176 751 Planarity : 0.004 0.050 785 Dihedral : 4.952 50.379 692 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.34), residues: 565 helix: 2.20 (0.33), residues: 220 sheet: -0.86 (0.70), residues: 66 loop : -2.88 (0.29), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG g 102 TYR 0.019 0.001 TYR e 99 PHE 0.035 0.001 PHE b 40 TRP 0.004 0.001 TRP d 43 HIS 0.003 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 4724) covalent geometry : angle 0.63807 ( 6404) SS BOND : bond 0.00421 ( 9) SS BOND : angle 1.65819 ( 18) hydrogen bonds : bond 0.04227 ( 223) hydrogen bonds : angle 4.02213 ( 648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: d 68 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7474 (mtp180) REVERT: d 70 ILE cc_start: 0.8556 (mp) cc_final: 0.8211 (tt) REVERT: e 36 TYR cc_start: 0.8013 (m-80) cc_final: 0.6809 (m-80) REVERT: e 98 CYS cc_start: 0.3610 (p) cc_final: 0.3292 (p) REVERT: f 110 PHE cc_start: 0.8126 (p90) cc_final: 0.7924 (p90) REVERT: f 120 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8316 (tm-30) REVERT: f 121 ASN cc_start: 0.8280 (p0) cc_final: 0.7877 (p0) REVERT: g 39 ASP cc_start: 0.8340 (p0) cc_final: 0.7800 (p0) REVERT: g 80 ASP cc_start: 0.8259 (m-30) cc_final: 0.7811 (t0) REVERT: m 267 LEU cc_start: 0.9321 (tp) cc_final: 0.9059 (tt) REVERT: m 286 LYS cc_start: 0.8483 (tppt) cc_final: 0.8217 (tptt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.0738 time to fit residues: 13.9453 Evaluate side-chains 124 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 12 optimal weight: 0.1980 chunk 4 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.181018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.161473 restraints weight = 7664.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.161119 restraints weight = 6909.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.161273 restraints weight = 6264.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.161271 restraints weight = 6095.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.161320 restraints weight = 5938.877| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4733 Z= 0.139 Angle : 0.669 6.544 6422 Z= 0.344 Chirality : 0.043 0.165 751 Planarity : 0.004 0.042 785 Dihedral : 5.059 51.176 692 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.34), residues: 565 helix: 2.14 (0.33), residues: 221 sheet: -0.81 (0.66), residues: 73 loop : -2.82 (0.30), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG f 101 TYR 0.014 0.001 TYR g 34 PHE 0.012 0.001 PHE g 118 TRP 0.005 0.001 TRP g 72 HIS 0.004 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4724) covalent geometry : angle 0.65966 ( 6404) SS BOND : bond 0.00441 ( 9) SS BOND : angle 2.24123 ( 18) hydrogen bonds : bond 0.04330 ( 223) hydrogen bonds : angle 3.94018 ( 648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: d 68 ARG cc_start: 0.7918 (mtp180) cc_final: 0.7662 (mtp180) REVERT: d 70 ILE cc_start: 0.8632 (mp) cc_final: 0.8350 (tt) REVERT: d 87 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7920 (tm-30) REVERT: e 36 TYR cc_start: 0.8034 (m-80) cc_final: 0.6937 (m-10) REVERT: e 98 CYS cc_start: 0.3453 (p) cc_final: 0.2986 (p) REVERT: f 120 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8316 (tm-30) REVERT: g 39 ASP cc_start: 0.8289 (p0) cc_final: 0.7824 (p0) REVERT: g 80 ASP cc_start: 0.8301 (m-30) cc_final: 0.7835 (t0) REVERT: m 267 LEU cc_start: 0.9359 (tp) cc_final: 0.9104 (tt) REVERT: m 286 LYS cc_start: 0.8417 (tppt) cc_final: 0.8214 (tptt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.0767 time to fit residues: 14.2796 Evaluate side-chains 124 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 0.1980 chunk 38 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.0170 chunk 11 optimal weight: 0.7980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN d 89 HIS e 92 GLN f 81 HIS ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.181554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.160488 restraints weight = 7839.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.161236 restraints weight = 6538.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.162091 restraints weight = 5737.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.162122 restraints weight = 5227.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.162648 restraints weight = 5172.758| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4733 Z= 0.125 Angle : 0.659 6.595 6422 Z= 0.335 Chirality : 0.043 0.172 751 Planarity : 0.004 0.047 785 Dihedral : 5.011 51.460 692 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.34), residues: 565 helix: 2.18 (0.33), residues: 220 sheet: -1.37 (0.60), residues: 89 loop : -2.65 (0.30), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG f 101 TYR 0.008 0.001 TYR n 266 PHE 0.022 0.001 PHE g 118 TRP 0.004 0.001 TRP f 59 HIS 0.002 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4724) covalent geometry : angle 0.65103 ( 6404) SS BOND : bond 0.00301 ( 9) SS BOND : angle 2.06275 ( 18) hydrogen bonds : bond 0.04014 ( 223) hydrogen bonds : angle 3.89625 ( 648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 28 ASP cc_start: 0.6893 (m-30) cc_final: 0.6253 (p0) REVERT: d 70 ILE cc_start: 0.8718 (mp) cc_final: 0.8392 (tt) REVERT: e 36 TYR cc_start: 0.7987 (m-80) cc_final: 0.7105 (m-10) REVERT: e 98 CYS cc_start: 0.3555 (p) cc_final: 0.2975 (p) REVERT: f 115 ARG cc_start: 0.8524 (tpt-90) cc_final: 0.8152 (tpt90) REVERT: f 120 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8297 (tm-30) REVERT: f 125 MET cc_start: 0.8085 (ppp) cc_final: 0.7763 (ppp) REVERT: g 39 ASP cc_start: 0.8003 (p0) cc_final: 0.7577 (p0) REVERT: g 80 ASP cc_start: 0.8237 (m-30) cc_final: 0.7861 (t0) REVERT: m 267 LEU cc_start: 0.9326 (tp) cc_final: 0.9076 (tt) REVERT: m 286 LYS cc_start: 0.8413 (tppt) cc_final: 0.8205 (tptt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.0740 time to fit residues: 13.5665 Evaluate side-chains 122 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 0.0370 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN f 81 HIS ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.176556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.163946 restraints weight = 7951.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.164217 restraints weight = 12394.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.164347 restraints weight = 9327.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.164316 restraints weight = 7606.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.164403 restraints weight = 7173.390| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4733 Z= 0.130 Angle : 0.652 6.536 6422 Z= 0.334 Chirality : 0.042 0.193 751 Planarity : 0.004 0.043 785 Dihedral : 5.043 51.152 692 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.34), residues: 565 helix: 2.30 (0.32), residues: 221 sheet: -1.29 (0.55), residues: 100 loop : -2.58 (0.31), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG g 82 TYR 0.011 0.001 TYR g 100 PHE 0.020 0.001 PHE g 118 TRP 0.004 0.001 TRP g 72 HIS 0.003 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4724) covalent geometry : angle 0.64477 ( 6404) SS BOND : bond 0.00421 ( 9) SS BOND : angle 1.93169 ( 18) hydrogen bonds : bond 0.03911 ( 223) hydrogen bonds : angle 3.85115 ( 648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 28 ASP cc_start: 0.6772 (m-30) cc_final: 0.6231 (p0) REVERT: d 68 ARG cc_start: 0.7683 (mtp-110) cc_final: 0.7462 (mtp180) REVERT: d 70 ILE cc_start: 0.8621 (mp) cc_final: 0.8389 (tt) REVERT: e 36 TYR cc_start: 0.7915 (m-80) cc_final: 0.6974 (m-10) REVERT: e 98 CYS cc_start: 0.3179 (p) cc_final: 0.2717 (p) REVERT: f 110 PHE cc_start: 0.8178 (p90) cc_final: 0.7935 (p90) REVERT: f 120 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8352 (tm-30) REVERT: g 39 ASP cc_start: 0.7462 (p0) cc_final: 0.7127 (p0) REVERT: m 267 LEU cc_start: 0.9337 (tp) cc_final: 0.9079 (tt) REVERT: m 286 LYS cc_start: 0.8392 (tppt) cc_final: 0.8157 (tptt) REVERT: n 265 MET cc_start: 0.8863 (mmm) cc_final: 0.8173 (ttm) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.0619 time to fit residues: 11.1811 Evaluate side-chains 120 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN f 81 HIS n 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.174279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.153081 restraints weight = 7920.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.154274 restraints weight = 6291.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.155332 restraints weight = 5316.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.156261 restraints weight = 4678.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.156375 restraints weight = 4223.892| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4733 Z= 0.132 Angle : 0.673 7.453 6422 Z= 0.342 Chirality : 0.042 0.185 751 Planarity : 0.004 0.039 785 Dihedral : 5.058 49.600 692 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.34), residues: 565 helix: 2.16 (0.32), residues: 221 sheet: -1.39 (0.60), residues: 87 loop : -2.53 (0.31), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG f 101 TYR 0.009 0.001 TYR e 36 PHE 0.018 0.001 PHE g 118 TRP 0.003 0.001 TRP e 59 HIS 0.003 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4724) covalent geometry : angle 0.66322 ( 6404) SS BOND : bond 0.00331 ( 9) SS BOND : angle 2.26256 ( 18) hydrogen bonds : bond 0.03934 ( 223) hydrogen bonds : angle 3.92571 ( 648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 28 ASP cc_start: 0.6993 (m-30) cc_final: 0.6325 (p0) REVERT: d 68 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.7551 (mtp-110) REVERT: d 70 ILE cc_start: 0.8791 (mp) cc_final: 0.8437 (tt) REVERT: e 36 TYR cc_start: 0.7720 (m-80) cc_final: 0.6451 (m-10) REVERT: e 49 CYS cc_start: 0.6430 (t) cc_final: 0.6163 (t) REVERT: e 98 CYS cc_start: 0.3596 (p) cc_final: 0.3354 (p) REVERT: f 120 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8357 (tm-30) REVERT: g 34 TYR cc_start: 0.6912 (t80) cc_final: 0.6702 (t80) REVERT: g 39 ASP cc_start: 0.7996 (p0) cc_final: 0.7524 (p0) REVERT: g 82 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8198 (mtt90) REVERT: m 267 LEU cc_start: 0.9284 (tp) cc_final: 0.9020 (tt) REVERT: m 286 LYS cc_start: 0.8469 (tppt) cc_final: 0.8187 (tptt) REVERT: n 265 MET cc_start: 0.8712 (mmm) cc_final: 0.8246 (ttm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.0745 time to fit residues: 13.3192 Evaluate side-chains 119 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 0.5980 chunk 7 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN f 81 HIS n 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.174992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153884 restraints weight = 7670.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.155465 restraints weight = 6035.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.156470 restraints weight = 5010.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.157430 restraints weight = 4367.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.158215 restraints weight = 3877.413| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4733 Z= 0.139 Angle : 0.697 7.161 6422 Z= 0.354 Chirality : 0.043 0.185 751 Planarity : 0.004 0.039 785 Dihedral : 5.144 50.688 692 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.34), residues: 565 helix: 2.17 (0.32), residues: 219 sheet: -1.25 (0.65), residues: 74 loop : -2.55 (0.31), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG f 101 TYR 0.012 0.001 TYR f 113 PHE 0.017 0.001 PHE g 118 TRP 0.007 0.001 TRP d 43 HIS 0.003 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4724) covalent geometry : angle 0.68711 ( 6404) SS BOND : bond 0.00438 ( 9) SS BOND : angle 2.30105 ( 18) hydrogen bonds : bond 0.03945 ( 223) hydrogen bonds : angle 3.89146 ( 648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 28 ASP cc_start: 0.6811 (m-30) cc_final: 0.6205 (p0) REVERT: d 68 ARG cc_start: 0.7973 (mtp-110) cc_final: 0.7424 (mtp-110) REVERT: d 70 ILE cc_start: 0.8842 (mp) cc_final: 0.8324 (tt) REVERT: d 87 GLN cc_start: 0.8333 (tm-30) cc_final: 0.8094 (tm-30) REVERT: e 36 TYR cc_start: 0.7719 (m-80) cc_final: 0.6491 (m-10) REVERT: e 49 CYS cc_start: 0.6462 (t) cc_final: 0.6246 (t) REVERT: e 98 CYS cc_start: 0.3385 (p) cc_final: 0.2991 (p) REVERT: f 120 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8327 (tm-30) REVERT: g 39 ASP cc_start: 0.7955 (p0) cc_final: 0.7551 (p0) REVERT: g 61 MET cc_start: 0.1504 (tpt) cc_final: 0.1186 (tpt) REVERT: g 82 ARG cc_start: 0.8575 (mtt180) cc_final: 0.8174 (mtt90) REVERT: m 267 LEU cc_start: 0.9338 (tp) cc_final: 0.9086 (tt) REVERT: m 286 LYS cc_start: 0.8405 (tppt) cc_final: 0.8173 (tptt) REVERT: n 265 MET cc_start: 0.8723 (mmm) cc_final: 0.8318 (ttm) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.0739 time to fit residues: 13.3621 Evaluate side-chains 120 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN f 81 HIS ** n 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.170236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.154226 restraints weight = 7920.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.154640 restraints weight = 13421.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.154944 restraints weight = 10732.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.155018 restraints weight = 8401.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.155263 restraints weight = 7670.357| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4733 Z= 0.168 Angle : 0.750 10.945 6422 Z= 0.382 Chirality : 0.045 0.187 751 Planarity : 0.004 0.041 785 Dihedral : 5.339 46.458 692 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.34), residues: 565 helix: 1.85 (0.32), residues: 219 sheet: -1.58 (0.60), residues: 87 loop : -2.55 (0.31), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG f 115 TYR 0.020 0.002 TYR g 34 PHE 0.021 0.002 PHE b 40 TRP 0.007 0.001 TRP g 55 HIS 0.005 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 4724) covalent geometry : angle 0.74066 ( 6404) SS BOND : bond 0.00378 ( 9) SS BOND : angle 2.29309 ( 18) hydrogen bonds : bond 0.04509 ( 223) hydrogen bonds : angle 4.07702 ( 648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: d 68 ARG cc_start: 0.7985 (mtp-110) cc_final: 0.7599 (mtp-110) REVERT: e 36 TYR cc_start: 0.7771 (m-80) cc_final: 0.6509 (m-10) REVERT: e 49 CYS cc_start: 0.6262 (t) cc_final: 0.5852 (t) REVERT: f 110 PHE cc_start: 0.8339 (p90) cc_final: 0.8056 (p90) REVERT: f 120 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8306 (tm-30) REVERT: g 34 TYR cc_start: 0.7115 (t80) cc_final: 0.6906 (t80) REVERT: g 39 ASP cc_start: 0.7893 (p0) cc_final: 0.7424 (p0) REVERT: m 267 LEU cc_start: 0.9307 (tp) cc_final: 0.9057 (tt) REVERT: m 284 THR cc_start: 0.8871 (m) cc_final: 0.8667 (m) REVERT: m 286 LYS cc_start: 0.8453 (tppt) cc_final: 0.8155 (tptt) REVERT: n 265 MET cc_start: 0.8948 (mmm) cc_final: 0.8249 (ttm) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.0741 time to fit residues: 12.9880 Evaluate side-chains 119 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 10.0000 chunk 18 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 HIS n 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.173400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.151565 restraints weight = 7785.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.152834 restraints weight = 6302.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.153586 restraints weight = 5372.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.154609 restraints weight = 4778.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.154609 restraints weight = 4347.000| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4733 Z= 0.137 Angle : 0.717 8.816 6422 Z= 0.363 Chirality : 0.043 0.188 751 Planarity : 0.004 0.048 785 Dihedral : 5.315 49.746 692 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.34), residues: 565 helix: 2.15 (0.32), residues: 218 sheet: -1.42 (0.57), residues: 91 loop : -2.44 (0.32), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG e 115 TYR 0.018 0.001 TYR g 34 PHE 0.020 0.002 PHE b 40 TRP 0.004 0.001 TRP g 72 HIS 0.003 0.001 HIS f 61 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 4724) covalent geometry : angle 0.70844 ( 6404) SS BOND : bond 0.00377 ( 9) SS BOND : angle 2.22374 ( 18) hydrogen bonds : bond 0.04063 ( 223) hydrogen bonds : angle 3.90220 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 987.64 seconds wall clock time: 17 minutes 44.30 seconds (1064.30 seconds total)