Starting phenix.real_space_refine on Sat May 10 01:45:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yc0_39128/05_2025/8yc0_39128.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yc0_39128/05_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_39128/05_2025/8yc0_39128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yc0_39128/05_2025/8yc0_39128.map" model { file = "/net/cci-nas-00/data/ceres_data/8yc0_39128/05_2025/8yc0_39128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yc0_39128/05_2025/8yc0_39128.cif" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 3.12, per 1000 atoms: 0.67 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: 1.04 Conformation dependent library (CDL) restraints added in 518.3 milliseconds 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: 0.43 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: 1.09 Time building geometry restraints manager: 1.21 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: 0.490 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.740 Find NCS groups from input model: 0.110 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.590 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (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 TRP 0.016 0.001 TRP d 43 HIS 0.004 0.001 HIS f 61 PHE 0.020 0.001 PHE g 118 TYR 0.016 0.001 TYR b 42 ARG 0.005 0.000 ARG d 63 Details of bonding type rmsd hydrogen bonds : bond 0.17723 ( 223) hydrogen bonds : angle 6.27538 ( 648) SS BOND : bond 0.00354 ( 9) SS BOND : angle 2.20836 ( 18) covalent geometry : bond 0.00354 ( 4724) covalent geometry : angle 0.77359 ( 6404) *********************** 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 : 0.467 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: 0.6834 (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: 0.7838 (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: 0.5597 (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: 0.4753 (ptp) REVERT: g 38 GLU cc_start: 0.8295 (pm20) cc_final: 0.8071 (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: 0.6954 (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: 0.1884 time to fit residues: 35.3635 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 : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.184885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.159468 restraints weight = 8717.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.159508 restraints weight = 13106.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.160672 restraints weight = 10109.338| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4733 Z= 0.170 Angle : 0.714 5.993 6422 Z= 0.372 Chirality : 0.045 0.171 751 Planarity : 0.005 0.055 785 Dihedral : 5.114 50.333 692 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.19 % Allowed : 4.07 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.34), residues: 565 helix: 2.03 (0.33), residues: 217 sheet: -1.30 (0.61), residues: 82 loop : -3.01 (0.30), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP e 59 HIS 0.008 0.002 HIS f 61 PHE 0.014 0.001 PHE b 40 TYR 0.011 0.002 TYR d 79 ARG 0.003 0.001 ARG e 101 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 223) hydrogen bonds : angle 4.53383 ( 648) SS BOND : bond 0.00371 ( 9) SS BOND : angle 2.06632 ( 18) covalent geometry : bond 0.00388 ( 4724) covalent geometry : angle 0.70642 ( 6404) *********************** 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 169 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 36 TYR cc_start: 0.8125 (m-80) cc_final: 0.6936 (m-10) REVERT: e 117 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7378 (ttt180) REVERT: f 110 PHE cc_start: 0.8216 (p90) cc_final: 0.7907 (p90) REVERT: f 121 ASN cc_start: 0.8333 (m-40) cc_final: 0.7000 (m-40) REVERT: f 128 MET cc_start: 0.6397 (mpp) cc_final: 0.6174 (mmt) REVERT: g 39 ASP cc_start: 0.8354 (p0) cc_final: 0.7962 (p0) REVERT: g 80 ASP cc_start: 0.8348 (m-30) cc_final: 0.8123 (t0) REVERT: m 286 LYS cc_start: 0.8595 (tppt) cc_final: 0.8362 (tptt) REVERT: n 259 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7938 (t0) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.1681 time to fit residues: 35.2051 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 : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 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 89 HIS 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 = 0.4180 r_free = 0.4180 target = 0.181133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.159021 restraints weight = 7630.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.159692 restraints weight = 6498.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.159692 restraints weight = 5897.983| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4733 Z= 0.134 Angle : 0.656 6.325 6422 Z= 0.338 Chirality : 0.043 0.201 751 Planarity : 0.005 0.056 785 Dihedral : 5.006 50.604 692 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.34), residues: 565 helix: 2.31 (0.32), residues: 218 sheet: -1.21 (0.62), residues: 78 loop : -2.95 (0.29), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 43 HIS 0.004 0.001 HIS d 89 PHE 0.038 0.001 PHE b 40 TYR 0.012 0.001 TYR g 34 ARG 0.005 0.001 ARG g 102 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 223) hydrogen bonds : angle 4.19647 ( 648) SS BOND : bond 0.00411 ( 9) SS BOND : angle 2.03161 ( 18) covalent geometry : bond 0.00290 ( 4724) covalent geometry : angle 0.64757 ( 6404) *********************** 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 155 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: e 36 TYR cc_start: 0.7869 (m-80) cc_final: 0.6491 (m-80) REVERT: e 49 CYS cc_start: 0.6425 (t) cc_final: 0.5897 (t) REVERT: e 117 ARG cc_start: 0.7721 (mtp180) cc_final: 0.7377 (ttt180) REVERT: f 110 PHE cc_start: 0.8159 (p90) cc_final: 0.7950 (p90) REVERT: f 115 ARG cc_start: 0.8281 (ttt-90) cc_final: 0.8004 (tpt-90) REVERT: f 120 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7707 (tm-30) REVERT: f 121 ASN cc_start: 0.8177 (m-40) cc_final: 0.7512 (m-40) REVERT: f 125 MET cc_start: 0.8274 (ppp) cc_final: 0.8063 (ppp) REVERT: f 128 MET cc_start: 0.6208 (mpp) cc_final: 0.5858 (mmt) REVERT: g 39 ASP cc_start: 0.8137 (p0) cc_final: 0.7796 (p0) REVERT: g 80 ASP cc_start: 0.8309 (m-30) cc_final: 0.8019 (t0) REVERT: m 286 LYS cc_start: 0.8556 (tppt) cc_final: 0.8246 (tptt) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1759 time to fit residues: 33.8813 Evaluate side-chains 131 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.3980 chunk 51 optimal weight: 0.4980 chunk 27 optimal weight: 0.4980 chunk 37 optimal weight: 0.2980 chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN 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 = 0.4189 r_free = 0.4189 target = 0.182290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.162943 restraints weight = 7632.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.162122 restraints weight = 9431.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.162631 restraints weight = 9081.504| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3583 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= 0.127 Angle : 0.639 6.514 6422 Z= 0.333 Chirality : 0.042 0.183 751 Planarity : 0.005 0.052 785 Dihedral : 4.940 50.493 692 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.34), residues: 565 helix: 2.21 (0.32), residues: 220 sheet: -1.20 (0.62), residues: 78 loop : -2.85 (0.30), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP d 43 HIS 0.007 0.001 HIS d 89 PHE 0.035 0.001 PHE b 40 TYR 0.020 0.001 TYR e 99 ARG 0.005 0.001 ARG g 102 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 223) hydrogen bonds : angle 4.01490 ( 648) SS BOND : bond 0.00370 ( 9) SS BOND : angle 1.66516 ( 18) covalent geometry : bond 0.00268 ( 4724) covalent geometry : angle 0.63390 ( 6404) *********************** 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 151 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: d 70 ILE cc_start: 0.8523 (mp) cc_final: 0.8265 (tt) REVERT: e 36 TYR cc_start: 0.7917 (m-80) cc_final: 0.6794 (m-80) REVERT: e 98 CYS cc_start: 0.3337 (p) cc_final: 0.3022 (p) REVERT: e 117 ARG cc_start: 0.7561 (mtp180) cc_final: 0.7272 (ttt180) REVERT: f 89 GLU cc_start: 0.7477 (tt0) cc_final: 0.6672 (tt0) REVERT: f 110 PHE cc_start: 0.8123 (p90) cc_final: 0.7862 (p90) REVERT: f 120 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7784 (tm-30) REVERT: f 121 ASN cc_start: 0.8121 (m-40) cc_final: 0.7294 (m-40) REVERT: f 128 MET cc_start: 0.6460 (mpp) cc_final: 0.5901 (mmt) REVERT: g 39 ASP cc_start: 0.8002 (p0) cc_final: 0.7566 (p0) REVERT: g 57 LYS cc_start: 0.7235 (tptm) cc_final: 0.6985 (tptm) REVERT: m 267 LEU cc_start: 0.9375 (tp) cc_final: 0.9130 (tt) REVERT: m 286 LYS cc_start: 0.8518 (tppt) cc_final: 0.8210 (tptt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1725 time to fit residues: 32.0148 Evaluate side-chains 129 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN e 92 GLN f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4161 r_free = 0.4161 target = 0.179024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.158356 restraints weight = 7796.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.157999 restraints weight = 9360.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.158200 restraints weight = 8823.938| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.3838 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= 0.148 Angle : 0.677 6.731 6422 Z= 0.347 Chirality : 0.043 0.173 751 Planarity : 0.004 0.041 785 Dihedral : 5.011 50.390 692 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.34), residues: 565 helix: 2.12 (0.33), residues: 221 sheet: -1.17 (0.60), residues: 83 loop : -2.83 (0.31), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP f 59 HIS 0.004 0.001 HIS f 61 PHE 0.010 0.001 PHE n 277 TYR 0.014 0.001 TYR g 34 ARG 0.008 0.001 ARG f 101 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 223) hydrogen bonds : angle 3.98381 ( 648) SS BOND : bond 0.00356 ( 9) SS BOND : angle 2.27987 ( 18) covalent geometry : bond 0.00334 ( 4724) covalent geometry : angle 0.66716 ( 6404) *********************** 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 153 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: a 47 THR cc_start: 0.8388 (m) cc_final: 0.8168 (t) REVERT: d 68 ARG cc_start: 0.8039 (mtp180) cc_final: 0.7631 (mtp180) REVERT: d 70 ILE cc_start: 0.8666 (mp) cc_final: 0.8351 (tt) REVERT: e 36 TYR cc_start: 0.8029 (m-80) cc_final: 0.6889 (m-10) REVERT: e 98 CYS cc_start: 0.3410 (p) cc_final: 0.2987 (p) REVERT: e 117 ARG cc_start: 0.7694 (mtp180) cc_final: 0.7397 (ttt180) REVERT: f 110 PHE cc_start: 0.8133 (p90) cc_final: 0.7908 (p90) REVERT: f 120 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7634 (tm-30) REVERT: f 121 ASN cc_start: 0.8170 (m-40) cc_final: 0.7197 (m110) REVERT: f 128 MET cc_start: 0.6038 (mpp) cc_final: 0.5669 (mmt) REVERT: g 39 ASP cc_start: 0.8134 (p0) cc_final: 0.7673 (p0) REVERT: g 57 LYS cc_start: 0.7449 (tptm) cc_final: 0.7246 (tptm) REVERT: m 267 LEU cc_start: 0.9403 (tp) cc_final: 0.9141 (tt) REVERT: m 286 LYS cc_start: 0.8457 (tppt) cc_final: 0.8243 (tptt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1760 time to fit residues: 33.5262 Evaluate side-chains 125 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 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 ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4096 r_free = 0.4096 target = 0.172869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.151826 restraints weight = 7857.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.152546 restraints weight = 6537.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.153445 restraints weight = 5751.756| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4733 Z= 0.132 Angle : 0.657 6.816 6422 Z= 0.336 Chirality : 0.043 0.182 751 Planarity : 0.004 0.047 785 Dihedral : 4.992 51.037 692 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.34), residues: 565 helix: 2.14 (0.32), residues: 220 sheet: -1.33 (0.61), residues: 89 loop : -2.68 (0.31), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP f 59 HIS 0.004 0.001 HIS d 89 PHE 0.011 0.001 PHE b 40 TYR 0.006 0.001 TYR f 113 ARG 0.007 0.001 ARG f 101 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 223) hydrogen bonds : angle 3.96240 ( 648) SS BOND : bond 0.00370 ( 9) SS BOND : angle 1.99211 ( 18) covalent geometry : bond 0.00296 ( 4724) covalent geometry : angle 0.64949 ( 6404) *********************** 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 145 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.519 Fit side-chains REVERT: a 28 ASP cc_start: 0.7091 (m-30) cc_final: 0.6324 (p0) REVERT: d 70 ILE cc_start: 0.8681 (mp) cc_final: 0.8404 (tt) REVERT: e 36 TYR cc_start: 0.8042 (m-80) cc_final: 0.7008 (m-10) REVERT: e 98 CYS cc_start: 0.3657 (p) cc_final: 0.3100 (p) REVERT: e 117 ARG cc_start: 0.7878 (mtp180) cc_final: 0.7569 (ttt180) REVERT: f 120 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7762 (tm-30) REVERT: f 121 ASN cc_start: 0.8219 (m-40) cc_final: 0.7166 (m-40) REVERT: f 128 MET cc_start: 0.5912 (mpp) cc_final: 0.5530 (mmt) REVERT: g 39 ASP cc_start: 0.8098 (p0) cc_final: 0.7679 (p0) REVERT: g 103 MET cc_start: 0.8069 (mmm) cc_final: 0.7866 (mmm) REVERT: m 267 LEU cc_start: 0.9348 (tp) cc_final: 0.9120 (tt) REVERT: m 286 LYS cc_start: 0.8434 (tppt) cc_final: 0.8212 (tptt) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1772 time to fit residues: 31.8734 Evaluate side-chains 121 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** e 92 GLN f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4103 r_free = 0.4103 target = 0.173304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151603 restraints weight = 7846.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.152704 restraints weight = 6369.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153909 restraints weight = 5463.269| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4218 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= 0.132 Angle : 0.681 6.991 6422 Z= 0.347 Chirality : 0.043 0.191 751 Planarity : 0.004 0.043 785 Dihedral : 5.084 50.377 692 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.34), residues: 565 helix: 2.14 (0.33), residues: 221 sheet: -0.97 (0.62), residues: 86 loop : -2.69 (0.30), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP f 59 HIS 0.003 0.001 HIS f 61 PHE 0.010 0.001 PHE n 277 TYR 0.008 0.001 TYR f 113 ARG 0.007 0.001 ARG f 101 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 223) hydrogen bonds : angle 3.93538 ( 648) SS BOND : bond 0.00418 ( 9) SS BOND : angle 1.98912 ( 18) covalent geometry : bond 0.00292 ( 4724) covalent geometry : angle 0.67342 ( 6404) *********************** 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 143 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.652 Fit side-chains REVERT: a 28 ASP cc_start: 0.7026 (m-30) cc_final: 0.6325 (p0) REVERT: d 70 ILE cc_start: 0.8693 (mp) cc_final: 0.8442 (tt) REVERT: e 36 TYR cc_start: 0.8037 (m-80) cc_final: 0.7035 (m-10) REVERT: e 98 CYS cc_start: 0.3701 (p) cc_final: 0.3130 (p) REVERT: e 117 ARG cc_start: 0.7816 (mtp180) cc_final: 0.7490 (ttt180) REVERT: f 46 ILE cc_start: 0.7698 (mm) cc_final: 0.7484 (mm) REVERT: f 110 PHE cc_start: 0.8141 (p90) cc_final: 0.7899 (p90) REVERT: f 120 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7761 (tm-30) REVERT: f 121 ASN cc_start: 0.8187 (m-40) cc_final: 0.7160 (m-40) REVERT: f 128 MET cc_start: 0.5775 (mpp) cc_final: 0.5548 (mmt) REVERT: g 39 ASP cc_start: 0.8036 (p0) cc_final: 0.7595 (p0) REVERT: g 80 ASP cc_start: 0.8073 (t0) cc_final: 0.7018 (t0) REVERT: m 267 LEU cc_start: 0.9363 (tp) cc_final: 0.9129 (tt) REVERT: m 286 LYS cc_start: 0.8466 (tppt) cc_final: 0.8249 (tptt) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1678 time to fit residues: 30.0648 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 : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** e 92 GLN f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4103 r_free = 0.4103 target = 0.173666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.152133 restraints weight = 7725.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.153369 restraints weight = 6159.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.154528 restraints weight = 5194.576| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4733 Z= 0.130 Angle : 0.675 7.211 6422 Z= 0.343 Chirality : 0.042 0.162 751 Planarity : 0.004 0.042 785 Dihedral : 5.032 50.382 692 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.35), residues: 565 helix: 2.23 (0.33), residues: 221 sheet: -1.05 (0.59), residues: 94 loop : -2.59 (0.32), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP f 59 HIS 0.003 0.001 HIS d 89 PHE 0.010 0.001 PHE n 277 TYR 0.010 0.001 TYR g 85 ARG 0.008 0.001 ARG g 82 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 223) hydrogen bonds : angle 3.88521 ( 648) SS BOND : bond 0.00360 ( 9) SS BOND : angle 2.34993 ( 18) covalent geometry : bond 0.00284 ( 4724) covalent geometry : angle 0.66404 ( 6404) *********************** 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 144 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.520 Fit side-chains REVERT: a 28 ASP cc_start: 0.6890 (m-30) cc_final: 0.6206 (p0) REVERT: d 70 ILE cc_start: 0.8757 (mp) cc_final: 0.8523 (tt) REVERT: e 36 TYR cc_start: 0.7984 (m-80) cc_final: 0.7048 (m-80) REVERT: e 98 CYS cc_start: 0.3668 (p) cc_final: 0.3102 (p) REVERT: e 117 ARG cc_start: 0.7803 (mtp180) cc_final: 0.7505 (ttt180) REVERT: f 46 ILE cc_start: 0.7605 (mm) cc_final: 0.7354 (mm) REVERT: f 106 GLU cc_start: 0.6302 (tp30) cc_final: 0.5987 (tp30) REVERT: f 110 PHE cc_start: 0.8022 (p90) cc_final: 0.7807 (p90) REVERT: f 120 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7640 (tm-30) REVERT: f 121 ASN cc_start: 0.8207 (m-40) cc_final: 0.7203 (m-40) REVERT: f 128 MET cc_start: 0.5754 (mpp) cc_final: 0.5519 (mmt) REVERT: g 39 ASP cc_start: 0.7946 (p0) cc_final: 0.7586 (p0) REVERT: m 267 LEU cc_start: 0.9333 (tp) cc_final: 0.9100 (tt) REVERT: m 286 LYS cc_start: 0.8452 (tppt) cc_final: 0.8226 (tptt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1716 time to fit residues: 30.7301 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 : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** e 92 GLN f 81 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4119 r_free = 0.4119 target = 0.175603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.155864 restraints weight = 7650.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.156896 restraints weight = 6116.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.157894 restraints weight = 5217.106| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.4569 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= 0.128 Angle : 0.684 7.128 6422 Z= 0.347 Chirality : 0.043 0.165 751 Planarity : 0.004 0.041 785 Dihedral : 5.093 51.624 692 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.35), residues: 565 helix: 2.09 (0.32), residues: 221 sheet: -1.12 (0.59), residues: 94 loop : -2.51 (0.32), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 43 HIS 0.003 0.001 HIS d 89 PHE 0.014 0.001 PHE b 40 TYR 0.020 0.001 TYR g 34 ARG 0.006 0.001 ARG e 115 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 223) hydrogen bonds : angle 3.86774 ( 648) SS BOND : bond 0.00361 ( 9) SS BOND : angle 2.20317 ( 18) covalent geometry : bond 0.00282 ( 4724) covalent geometry : angle 0.67514 ( 6404) *********************** 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 147 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.506 Fit side-chains REVERT: a 28 ASP cc_start: 0.6943 (m-30) cc_final: 0.6182 (p0) REVERT: d 68 ARG cc_start: 0.7846 (mtp-110) cc_final: 0.7231 (mtp-110) REVERT: d 70 ILE cc_start: 0.8809 (mp) cc_final: 0.8339 (tt) REVERT: e 36 TYR cc_start: 0.7683 (m-80) cc_final: 0.6496 (m-10) REVERT: e 98 CYS cc_start: 0.3483 (p) cc_final: 0.3221 (p) REVERT: e 117 ARG cc_start: 0.7861 (mtp180) cc_final: 0.7597 (ttt180) REVERT: f 46 ILE cc_start: 0.7479 (mm) cc_final: 0.7204 (mm) REVERT: f 110 PHE cc_start: 0.8056 (p90) cc_final: 0.7810 (p90) REVERT: f 115 ARG cc_start: 0.8612 (tpt-90) cc_final: 0.8248 (tpt90) REVERT: f 120 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7608 (tm-30) REVERT: f 121 ASN cc_start: 0.8169 (m-40) cc_final: 0.7143 (m-40) REVERT: g 39 ASP cc_start: 0.7987 (p0) cc_final: 0.7585 (p0) REVERT: g 61 MET cc_start: 0.1782 (tpt) cc_final: 0.1502 (tpt) REVERT: g 77 ASN cc_start: 0.8873 (p0) cc_final: 0.8662 (p0) REVERT: g 95 LYS cc_start: 0.7508 (mtpt) cc_final: 0.7271 (mtpp) REVERT: m 267 LEU cc_start: 0.9304 (tp) cc_final: 0.9070 (tt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1754 time to fit residues: 32.0370 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 : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN ** d 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 92 GLN ** f 60 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.174421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.153583 restraints weight = 7718.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.154748 restraints weight = 6279.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.155408 restraints weight = 5407.619| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.4642 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= 0.134 Angle : 0.710 7.920 6422 Z= 0.355 Chirality : 0.043 0.182 751 Planarity : 0.004 0.061 785 Dihedral : 5.126 49.282 692 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.35), residues: 565 helix: 2.28 (0.33), residues: 221 sheet: -1.18 (0.58), residues: 94 loop : -2.51 (0.32), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP e 59 HIS 0.003 0.001 HIS d 89 PHE 0.010 0.001 PHE n 277 TYR 0.015 0.001 TYR g 85 ARG 0.014 0.001 ARG f 101 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 223) hydrogen bonds : angle 3.87482 ( 648) SS BOND : bond 0.00370 ( 9) SS BOND : angle 2.25710 ( 18) covalent geometry : bond 0.00302 ( 4724) covalent geometry : angle 0.70117 ( 6404) ********************** 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 143 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.496 Fit side-chains REVERT: a 28 ASP cc_start: 0.6850 (m-30) cc_final: 0.6126 (p0) REVERT: a 40 PHE cc_start: 0.7996 (t80) cc_final: 0.7755 (t80) REVERT: d 70 ILE cc_start: 0.8737 (mp) cc_final: 0.8535 (tt) REVERT: e 36 TYR cc_start: 0.7647 (m-80) cc_final: 0.6485 (m-80) REVERT: e 98 CYS cc_start: 0.3450 (p) cc_final: 0.2991 (p) REVERT: e 117 ARG cc_start: 0.7893 (mtp180) cc_final: 0.7652 (ttt180) REVERT: f 46 ILE cc_start: 0.7448 (mm) cc_final: 0.7204 (mm) REVERT: f 110 PHE cc_start: 0.8085 (p90) cc_final: 0.7855 (p90) REVERT: f 120 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7677 (tm-30) REVERT: f 121 ASN cc_start: 0.8151 (m-40) cc_final: 0.7178 (m-40) REVERT: g 39 ASP cc_start: 0.8016 (p0) cc_final: 0.7663 (p0) REVERT: g 61 MET cc_start: 0.1632 (tpt) cc_final: 0.1318 (tpt) REVERT: g 84 MET cc_start: 0.7977 (mmt) cc_final: 0.7692 (mmt) REVERT: g 95 LYS cc_start: 0.7651 (mtpt) cc_final: 0.7417 (mtpp) REVERT: m 267 LEU cc_start: 0.9293 (tp) cc_final: 0.9063 (tt) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1642 time to fit residues: 29.4729 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 : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** 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 = 0.4072 r_free = 0.4072 target = 0.170639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.150446 restraints weight = 7829.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.151370 restraints weight = 6461.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.152562 restraints weight = 5602.973| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4733 Z= 0.141 Angle : 0.735 8.385 6422 Z= 0.367 Chirality : 0.044 0.161 751 Planarity : 0.004 0.052 785 Dihedral : 5.144 48.598 692 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.34), residues: 565 helix: 2.06 (0.32), residues: 221 sheet: -1.40 (0.60), residues: 87 loop : -2.53 (0.32), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 72 HIS 0.004 0.001 HIS d 89 PHE 0.014 0.001 PHE b 40 TYR 0.020 0.002 TYR g 34 ARG 0.010 0.001 ARG f 101 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 223) hydrogen bonds : angle 3.93948 ( 648) SS BOND : bond 0.00395 ( 9) SS BOND : angle 2.25826 ( 18) covalent geometry : bond 0.00323 ( 4724) covalent geometry : angle 0.72584 ( 6404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1826.09 seconds wall clock time: 32 minutes 31.63 seconds (1951.63 seconds total)