Starting phenix.real_space_refine on Tue Mar 3 13:30:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j5l_61145/03_2026/9j5l_61145.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j5l_61145/03_2026/9j5l_61145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j5l_61145/03_2026/9j5l_61145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j5l_61145/03_2026/9j5l_61145.map" model { file = "/net/cci-nas-00/data/ceres_data/9j5l_61145/03_2026/9j5l_61145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j5l_61145/03_2026/9j5l_61145.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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 31 5.16 5 C 3148 2.51 5 N 859 2.21 5 O 999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5037 Number of models: 1 Model: "" Number of chains: 10 Chain: "2" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1158 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 1, 'TRANS': 141} Chain breaks: 1 Chain: "B" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 789 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "C" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 892 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "D" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 799 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "E" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 905 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "J" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "1" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 371 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain breaks: 1 Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Classifications: {'peptide': 1} Chain: "2" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.31, per 1000 atoms: 0.26 Number of scatterers: 5037 At special positions: 0 Unit cell: (94.76, 81.88, 103.04, 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 31 16.00 O 999 8.00 N 859 7.00 C 3148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS 2 93 " - pdb=" SG CYS 1 307 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 124 " - pdb=" SG CYS H 62 " distance=2.15 Simple disulfide: pdb=" SG CYS 2 137 " - pdb=" SG CYS 1 4 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 108 " - pdb=" SG CYS 1 20 " distance=2.13 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 Links applied NAG-ASN " NAG 1 402 " - " ASN 1 11 " Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 323.2 milliseconds 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1178 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 14 sheets defined 14.7% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain '2' and resid 39 through 62 removed outlier: 3.757A pdb=" N THR 2 61 " --> pdb=" O GLU 2 57 " (cutoff:3.500A) Processing helix chain '2' and resid 92 through 126 removed outlier: 3.611A pdb=" N ALA 2 96 " --> pdb=" O TRP 2 92 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU 2 102 " --> pdb=" O LEU 2 98 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU 2 103 " --> pdb=" O LEU 2 99 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS 2 111 " --> pdb=" O THR 2 107 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP 2 112 " --> pdb=" O LEU 2 108 " (cutoff:3.500A) Processing helix chain '2' and resid 145 through 155 Processing helix chain '2' and resid 158 through 174 removed outlier: 3.655A pdb=" N TYR 2 162 " --> pdb=" O ASP 2 158 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU 2 164 " --> pdb=" O PRO 2 160 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU 2 165 " --> pdb=" O LYS 2 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 115 Processing sheet with id=AA1, first strand: chain '2' and resid 31 through 36 removed outlier: 3.588A pdb=" N GLY 1 6 " --> pdb=" O GLY 2 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 9 through 11 Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 18 Processing sheet with id=AA4, first strand: chain 'B' and resid 21 through 23 removed outlier: 3.543A pdb=" N CYS B 22 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER B 66 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 49 removed outlier: 7.103A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.866A pdb=" N CYS C 22 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.693A pdb=" N GLU C 10 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 118 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 92 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.693A pdb=" N GLU C 10 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR C 118 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 92 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL C 110 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 7.139A pdb=" N VAL D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TYR D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 17 through 21 Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.309A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N MET E 34 " --> pdb=" O PHE E 50 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 35 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA E 92 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL E 118 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '1' and resid 15 through 16 Processing sheet with id=AB5, first strand: chain '1' and resid 29 through 31 183 hydrogen bonds defined for protein. 489 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: 0.68 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1128 1.33 - 1.45: 1218 1.45 - 1.57: 2746 1.57 - 1.69: 0 1.69 - 1.81: 43 Bond restraints: 5135 Sorted by residual: bond pdb=" CA SER 2 54 " pdb=" CB SER 2 54 " ideal model delta sigma weight residual 1.528 1.480 0.048 1.56e-02 4.11e+03 9.52e+00 bond pdb=" N VAL 1 19 " pdb=" CA VAL 1 19 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.28e+00 bond pdb=" N ILE C 74 " pdb=" CA ILE C 74 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.77e+00 bond pdb=" N LYS 2 58 " pdb=" CA LYS 2 58 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.18e-02 7.18e+03 7.70e+00 bond pdb=" N ASP B 61 " pdb=" CA ASP B 61 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.10e-02 8.26e+03 7.66e+00 ... (remaining 5130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 6308 1.32 - 2.65: 469 2.65 - 3.97: 149 3.97 - 5.29: 27 5.29 - 6.61: 2 Bond angle restraints: 6955 Sorted by residual: angle pdb=" CA GLU 2 103 " pdb=" C GLU 2 103 " pdb=" O GLU 2 103 " ideal model delta sigma weight residual 120.55 116.37 4.18 1.06e+00 8.90e-01 1.55e+01 angle pdb=" N GLU 2 103 " pdb=" CA GLU 2 103 " pdb=" C GLU 2 103 " ideal model delta sigma weight residual 111.28 107.10 4.18 1.09e+00 8.42e-01 1.47e+01 angle pdb=" CA ASP 1 14 " pdb=" C ASP 1 14 " pdb=" O ASP 1 14 " ideal model delta sigma weight residual 121.55 117.49 4.06 1.06e+00 8.90e-01 1.46e+01 angle pdb=" CA LEU 2 101 " pdb=" C LEU 2 101 " pdb=" O LEU 2 101 " ideal model delta sigma weight residual 120.82 116.86 3.96 1.05e+00 9.07e-01 1.42e+01 angle pdb=" N MET 2 149 " pdb=" CA MET 2 149 " pdb=" C MET 2 149 " ideal model delta sigma weight residual 111.07 107.07 4.00 1.07e+00 8.73e-01 1.40e+01 ... (remaining 6950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 2753 16.65 - 33.31: 231 33.31 - 49.96: 58 49.96 - 66.62: 15 66.62 - 83.27: 11 Dihedral angle restraints: 3068 sinusoidal: 1215 harmonic: 1853 Sorted by residual: dihedral pdb=" CB CYS J 108 " pdb=" SG CYS J 108 " pdb=" SG CYS 1 20 " pdb=" CB CYS 1 20 " ideal model delta sinusoidal sigma weight residual 93.00 176.27 -83.27 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS 2 93 " pdb=" SG CYS 2 93 " pdb=" SG CYS 1 307 " pdb=" CB CYS 1 307 " ideal model delta sinusoidal sigma weight residual 93.00 123.93 -30.93 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CB CYS 2 124 " pdb=" SG CYS 2 124 " pdb=" SG CYS H 62 " pdb=" CB CYS H 62 " ideal model delta sinusoidal sigma weight residual -86.00 -115.24 29.24 1 1.00e+01 1.00e-02 1.22e+01 ... (remaining 3065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.314: 773 0.314 - 0.628: 0 0.628 - 0.943: 0 0.943 - 1.257: 0 1.257 - 1.571: 1 Chirality restraints: 774 Sorted by residual: chirality pdb=" C1 NAG 1 402 " pdb=" ND2 ASN 1 11 " pdb=" C2 NAG 1 402 " pdb=" O5 NAG 1 402 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-01 2.50e+01 6.17e+01 chirality pdb=" CA VAL 1 16 " pdb=" N VAL 1 16 " pdb=" C VAL 1 16 " pdb=" CB VAL 1 16 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE J 109 " pdb=" N ILE J 109 " pdb=" C ILE J 109 " pdb=" CB ILE J 109 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 771 not shown) Planarity restraints: 892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG 1 401 " 0.348 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG 1 401 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG 1 401 " 0.130 2.00e-02 2.50e+03 pdb=" N2 NAG 1 401 " -0.536 2.00e-02 2.50e+03 pdb=" O7 NAG 1 401 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY 2 8 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C GLY 2 8 " 0.062 2.00e-02 2.50e+03 pdb=" O GLY 2 8 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE 2 9 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU 2 57 " 0.018 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C GLU 2 57 " -0.061 2.00e-02 2.50e+03 pdb=" O GLU 2 57 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS 2 58 " 0.020 2.00e-02 2.50e+03 ... (remaining 889 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 38 2.59 - 3.17: 4203 3.17 - 3.75: 7049 3.75 - 4.32: 9759 4.32 - 4.90: 16819 Nonbonded interactions: 37868 Sorted by model distance: nonbonded pdb=" ND2 ASN 2 154 " pdb=" C1 NAG 2 201 " model vdw 2.013 3.550 nonbonded pdb=" ND2 ASN 1 23 " pdb=" C1 NAG 1 401 " model vdw 2.126 3.550 nonbonded pdb=" ND2 ASN 1 23 " pdb=" O5 NAG 1 401 " model vdw 2.317 3.120 nonbonded pdb=" O TYR 2 162 " pdb=" OG SER 2 166 " model vdw 2.330 3.040 nonbonded pdb=" O VAL E 48 " pdb=" OG SER E 49 " model vdw 2.330 3.040 ... (remaining 37863 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.900 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 : 0.006 0.118 5144 Z= 0.394 Angle : 1.037 35.352 6974 Z= 0.627 Chirality : 0.079 1.571 774 Planarity : 0.011 0.301 891 Dihedral : 14.147 82.123 1866 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.35), residues: 634 helix: 1.01 (0.60), residues: 88 sheet: 0.67 (0.39), residues: 209 loop : -0.99 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 1 312 TYR 0.013 0.001 TYR 2 94 PHE 0.010 0.001 PHE C 75 TRP 0.011 0.001 TRP 2 92 HIS 0.010 0.001 HIS 1 8 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 5135) covalent geometry : angle 0.82038 ( 6955) SS BOND : bond 0.05534 ( 8) SS BOND : angle 10.20589 ( 16) hydrogen bonds : bond 0.28457 ( 180) hydrogen bonds : angle 8.58355 ( 489) link_NAG-ASN : bond 0.01725 ( 1) link_NAG-ASN : angle 19.65478 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.9385 (tp) cc_final: 0.9054 (tp) REVERT: D 27 GLN cc_start: 0.8302 (mm-40) cc_final: 0.8093 (mm-40) REVERT: 1 1 ASP cc_start: 0.7686 (m-30) cc_final: 0.7006 (m-30) REVERT: 1 17 ASP cc_start: 0.8436 (p0) cc_final: 0.7832 (t0) REVERT: 1 18 THR cc_start: 0.8725 (t) cc_final: 0.8313 (p) REVERT: 1 21 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7524 (mm-30) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.5207 time to fit residues: 90.8296 Evaluate side-chains 122 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 53 ASN C 6 GLN D 37 GLN D 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.073526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.059595 restraints weight = 15410.128| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.72 r_work: 0.2945 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5144 Z= 0.165 Angle : 0.658 9.317 6974 Z= 0.342 Chirality : 0.043 0.137 774 Planarity : 0.004 0.037 891 Dihedral : 4.912 45.696 763 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.04 % Allowed : 21.32 % Favored : 74.63 % 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 are not related in a simple way. whole: 0.13 (0.34), residues: 634 helix: 2.08 (0.51), residues: 91 sheet: 0.80 (0.40), residues: 191 loop : -0.89 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 101 TYR 0.023 0.001 TYR D 91 PHE 0.020 0.002 PHE E 95 TRP 0.018 0.002 TRP B 36 HIS 0.003 0.001 HIS 1 8 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 5135) covalent geometry : angle 0.65712 ( 6955) SS BOND : bond 0.00504 ( 8) SS BOND : angle 0.92520 ( 16) hydrogen bonds : bond 0.05625 ( 180) hydrogen bonds : angle 5.22624 ( 489) link_NAG-ASN : bond 0.00405 ( 1) link_NAG-ASN : angle 0.62590 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 152 VAL cc_start: 0.9594 (t) cc_final: 0.9335 (p) REVERT: 2 158 ASP cc_start: 0.8336 (m-30) cc_final: 0.7968 (m-30) REVERT: B 37 TYR cc_start: 0.8975 (m-80) cc_final: 0.8768 (m-80) REVERT: D 17 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7670 (tm-30) REVERT: D 24 ARG cc_start: 0.8747 (ttm-80) cc_final: 0.8469 (ttm110) REVERT: D 70 GLU cc_start: 0.8584 (mp0) cc_final: 0.8246 (mp0) REVERT: D 79 GLN cc_start: 0.8644 (mt0) cc_final: 0.8362 (mp10) REVERT: D 82 ASP cc_start: 0.8453 (m-30) cc_final: 0.8119 (m-30) REVERT: E 103 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.5840 (mtp) REVERT: 1 17 ASP cc_start: 0.8608 (p0) cc_final: 0.8058 (t0) REVERT: 1 18 THR cc_start: 0.8501 (t) cc_final: 0.7918 (t) REVERT: 1 21 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7800 (mm-30) REVERT: 1 22 LYS cc_start: 0.9159 (mmtp) cc_final: 0.8646 (tptp) outliers start: 22 outliers final: 5 residues processed: 151 average time/residue: 0.4939 time to fit residues: 77.6597 Evaluate side-chains 128 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 113 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain E residue 103 MET Chi-restraints excluded: chain 1 residue 19 VAL Chi-restraints excluded: chain 1 residue 24 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.0010 chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 36 optimal weight: 0.0050 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN C 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.073294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059260 restraints weight = 15458.347| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.73 r_work: 0.2907 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 5144 Z= 0.143 Angle : 0.620 9.010 6974 Z= 0.326 Chirality : 0.042 0.150 774 Planarity : 0.004 0.067 891 Dihedral : 4.584 49.010 763 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.68 % Allowed : 22.43 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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 are not related in a simple way. whole: 0.19 (0.34), residues: 634 helix: 2.61 (0.51), residues: 91 sheet: 0.73 (0.39), residues: 197 loop : -0.96 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 101 TYR 0.015 0.001 TYR D 91 PHE 0.010 0.001 PHE E 95 TRP 0.011 0.001 TRP D 94 HIS 0.003 0.001 HIS 1 8 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5135) covalent geometry : angle 0.61969 ( 6955) SS BOND : bond 0.00369 ( 8) SS BOND : angle 0.70461 ( 16) hydrogen bonds : bond 0.05053 ( 180) hydrogen bonds : angle 4.79592 ( 489) link_NAG-ASN : bond 0.00374 ( 1) link_NAG-ASN : angle 0.78293 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 59 MET cc_start: 0.8567 (mmm) cc_final: 0.8309 (mmp) REVERT: 2 158 ASP cc_start: 0.8443 (m-30) cc_final: 0.8056 (m-30) REVERT: 2 172 LYS cc_start: 0.8494 (tmmm) cc_final: 0.8195 (tmmt) REVERT: C 73 ASP cc_start: 0.8183 (t0) cc_final: 0.7975 (t0) REVERT: C 82 GLU cc_start: 0.9099 (tp30) cc_final: 0.8760 (tp30) REVERT: D 17 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7825 (tp30) REVERT: D 70 GLU cc_start: 0.8543 (mp0) cc_final: 0.8259 (mp0) REVERT: D 79 GLN cc_start: 0.8578 (mt0) cc_final: 0.8186 (mp10) REVERT: 1 1 ASP cc_start: 0.8370 (m-30) cc_final: 0.8122 (m-30) REVERT: 1 18 THR cc_start: 0.8413 (t) cc_final: 0.8149 (t) REVERT: 1 21 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8001 (mm-30) REVERT: 1 22 LYS cc_start: 0.9173 (mmtp) cc_final: 0.8871 (tmtt) outliers start: 20 outliers final: 9 residues processed: 139 average time/residue: 0.5330 time to fit residues: 76.8698 Evaluate side-chains 126 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 40 SER Chi-restraints excluded: chain 2 residue 95 ILE Chi-restraints excluded: chain 2 residue 97 GLU Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 113 SER Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain 1 residue 19 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 25 HIS 2 125 GLN B 52 ASN 1 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.070568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.056509 restraints weight = 15399.201| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.69 r_work: 0.2840 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5144 Z= 0.192 Angle : 0.663 8.750 6974 Z= 0.351 Chirality : 0.044 0.160 774 Planarity : 0.005 0.065 891 Dihedral : 4.944 51.512 763 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.86 % Allowed : 22.79 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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 are not related in a simple way. whole: -0.02 (0.33), residues: 634 helix: 2.41 (0.52), residues: 91 sheet: 0.61 (0.38), residues: 196 loop : -1.09 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 24 TYR 0.022 0.002 TYR D 49 PHE 0.014 0.001 PHE E 95 TRP 0.007 0.001 TRP D 94 HIS 0.003 0.001 HIS 1 8 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 5135) covalent geometry : angle 0.66225 ( 6955) SS BOND : bond 0.00336 ( 8) SS BOND : angle 0.90250 ( 16) hydrogen bonds : bond 0.05479 ( 180) hydrogen bonds : angle 4.81978 ( 489) link_NAG-ASN : bond 0.00336 ( 1) link_NAG-ASN : angle 0.78544 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 59 MET cc_start: 0.8640 (mmm) cc_final: 0.8366 (mmp) REVERT: 2 158 ASP cc_start: 0.8646 (m-30) cc_final: 0.8266 (m-30) REVERT: C 73 ASP cc_start: 0.8236 (t0) cc_final: 0.7958 (t0) REVERT: C 82 GLU cc_start: 0.9086 (tp30) cc_final: 0.8772 (tp30) REVERT: D 17 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8229 (tp30) REVERT: D 24 ARG cc_start: 0.8706 (mtp-110) cc_final: 0.8312 (ttm110) REVERT: D 42 GLN cc_start: 0.8304 (mp10) cc_final: 0.8103 (mm-40) REVERT: D 70 GLU cc_start: 0.8465 (mp0) cc_final: 0.8227 (mp0) REVERT: D 79 GLN cc_start: 0.8645 (mt0) cc_final: 0.8082 (mp10) REVERT: D 82 ASP cc_start: 0.8641 (m-30) cc_final: 0.8326 (m-30) REVERT: J 107 ASN cc_start: 0.8789 (p0) cc_final: 0.8558 (p0) REVERT: 1 1 ASP cc_start: 0.8584 (m-30) cc_final: 0.8283 (m-30) REVERT: 1 21 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7926 (mm-30) REVERT: 1 22 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8788 (tmtt) outliers start: 21 outliers final: 11 residues processed: 132 average time/residue: 0.5397 time to fit residues: 73.9426 Evaluate side-chains 125 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 40 SER Chi-restraints excluded: chain 2 residue 97 GLU Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 113 SER Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain 1 residue 19 VAL Chi-restraints excluded: chain 1 residue 22 LYS Chi-restraints excluded: chain 1 residue 24 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 0.0270 chunk 50 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.0270 chunk 36 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.073032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.058760 restraints weight = 15331.178| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.75 r_work: 0.2899 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5144 Z= 0.126 Angle : 0.634 8.904 6974 Z= 0.331 Chirality : 0.042 0.159 774 Planarity : 0.004 0.060 891 Dihedral : 4.559 49.739 763 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.57 % Allowed : 24.63 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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 are not related in a simple way. whole: 0.11 (0.33), residues: 634 helix: 2.57 (0.51), residues: 91 sheet: 0.65 (0.38), residues: 192 loop : -0.99 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 101 TYR 0.025 0.001 TYR D 49 PHE 0.015 0.001 PHE C 75 TRP 0.009 0.001 TRP 2 92 HIS 0.002 0.000 HIS 1 8 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 5135) covalent geometry : angle 0.63465 ( 6955) SS BOND : bond 0.00299 ( 8) SS BOND : angle 0.53388 ( 16) hydrogen bonds : bond 0.04412 ( 180) hydrogen bonds : angle 4.48068 ( 489) link_NAG-ASN : bond 0.00306 ( 1) link_NAG-ASN : angle 0.70871 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 97 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8451 (pp20) REVERT: 2 98 LEU cc_start: 0.9321 (mt) cc_final: 0.8957 (mp) REVERT: 2 158 ASP cc_start: 0.8484 (m-30) cc_final: 0.8026 (m-30) REVERT: 2 172 LYS cc_start: 0.8584 (tmmm) cc_final: 0.8252 (tmmt) REVERT: C 73 ASP cc_start: 0.8075 (t0) cc_final: 0.7717 (t0) REVERT: C 82 GLU cc_start: 0.9070 (tp30) cc_final: 0.8802 (tp30) REVERT: D 24 ARG cc_start: 0.8693 (mtp-110) cc_final: 0.8392 (ttm110) REVERT: D 79 GLN cc_start: 0.8639 (mt0) cc_final: 0.8065 (mp10) REVERT: D 82 ASP cc_start: 0.8616 (m-30) cc_final: 0.8282 (m-30) REVERT: E 19 ARG cc_start: 0.9085 (ttt-90) cc_final: 0.8811 (mtp-110) REVERT: J 107 ASN cc_start: 0.8838 (p0) cc_final: 0.8629 (p0) REVERT: 1 1 ASP cc_start: 0.8461 (m-30) cc_final: 0.8187 (m-30) REVERT: 1 17 ASP cc_start: 0.8820 (p0) cc_final: 0.8151 (t0) REVERT: 1 21 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7809 (mm-30) REVERT: 1 22 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8656 (tmtt) outliers start: 14 outliers final: 7 residues processed: 133 average time/residue: 0.5217 time to fit residues: 72.1486 Evaluate side-chains 130 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 95 ILE Chi-restraints excluded: chain 2 residue 97 GLU Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain 1 residue 19 VAL Chi-restraints excluded: chain 1 residue 22 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 38 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 23 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 chunk 24 optimal weight: 0.6980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.073820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.059419 restraints weight = 15205.405| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.76 r_work: 0.2911 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5144 Z= 0.131 Angle : 0.664 9.508 6974 Z= 0.347 Chirality : 0.042 0.145 774 Planarity : 0.004 0.056 891 Dihedral : 4.501 51.618 763 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.57 % Allowed : 25.55 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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 are not related in a simple way. whole: 0.23 (0.33), residues: 634 helix: 2.68 (0.51), residues: 91 sheet: 0.79 (0.38), residues: 189 loop : -0.93 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 101 TYR 0.015 0.001 TYR E 80 PHE 0.015 0.001 PHE C 75 TRP 0.008 0.001 TRP 2 92 HIS 0.002 0.000 HIS 1 8 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5135) covalent geometry : angle 0.66444 ( 6955) SS BOND : bond 0.00289 ( 8) SS BOND : angle 0.61704 ( 16) hydrogen bonds : bond 0.04196 ( 180) hydrogen bonds : angle 4.34498 ( 489) link_NAG-ASN : bond 0.00278 ( 1) link_NAG-ASN : angle 0.69446 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 158 ASP cc_start: 0.8436 (m-30) cc_final: 0.8039 (m-30) REVERT: B 31 ARG cc_start: 0.9015 (pmm-80) cc_final: 0.8658 (pmm-80) REVERT: C 73 ASP cc_start: 0.8035 (t0) cc_final: 0.7614 (t0) REVERT: C 82 GLU cc_start: 0.9022 (tp30) cc_final: 0.8715 (tp30) REVERT: D 24 ARG cc_start: 0.8736 (mtp-110) cc_final: 0.8504 (ttm110) REVERT: D 42 GLN cc_start: 0.8281 (mp10) cc_final: 0.7945 (mm-40) REVERT: D 79 GLN cc_start: 0.8709 (mt0) cc_final: 0.8085 (mp10) REVERT: D 82 ASP cc_start: 0.8625 (m-30) cc_final: 0.8226 (m-30) REVERT: J 107 ASN cc_start: 0.8805 (p0) cc_final: 0.8589 (p0) REVERT: 1 1 ASP cc_start: 0.8413 (m-30) cc_final: 0.8146 (m-30) REVERT: 1 17 ASP cc_start: 0.8870 (p0) cc_final: 0.8225 (t0) REVERT: 1 21 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7868 (mm-30) REVERT: 1 22 LYS cc_start: 0.9182 (mmtp) cc_final: 0.8655 (tmtt) outliers start: 14 outliers final: 7 residues processed: 132 average time/residue: 0.5315 time to fit residues: 72.9069 Evaluate side-chains 129 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain 1 residue 19 VAL Chi-restraints excluded: chain 1 residue 314 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 0.0070 chunk 36 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.073683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.059511 restraints weight = 15049.670| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.71 r_work: 0.2913 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5144 Z= 0.134 Angle : 0.690 9.730 6974 Z= 0.354 Chirality : 0.042 0.157 774 Planarity : 0.004 0.049 891 Dihedral : 4.493 52.085 763 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.84 % Allowed : 27.76 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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 are not related in a simple way. whole: 0.15 (0.34), residues: 634 helix: 2.69 (0.52), residues: 91 sheet: 0.68 (0.38), residues: 192 loop : -0.98 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 17 TYR 0.025 0.001 TYR D 49 PHE 0.015 0.001 PHE C 75 TRP 0.008 0.001 TRP 2 92 HIS 0.004 0.001 HIS 1 8 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5135) covalent geometry : angle 0.69037 ( 6955) SS BOND : bond 0.00301 ( 8) SS BOND : angle 0.61102 ( 16) hydrogen bonds : bond 0.04103 ( 180) hydrogen bonds : angle 4.27279 ( 489) link_NAG-ASN : bond 0.00288 ( 1) link_NAG-ASN : angle 0.67290 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 158 ASP cc_start: 0.8417 (m-30) cc_final: 0.8031 (m-30) REVERT: C 73 ASP cc_start: 0.8030 (t0) cc_final: 0.7577 (t0) REVERT: C 82 GLU cc_start: 0.9015 (tp30) cc_final: 0.8704 (tp30) REVERT: D 24 ARG cc_start: 0.8697 (mtp-110) cc_final: 0.8424 (ttm110) REVERT: D 79 GLN cc_start: 0.8724 (mt0) cc_final: 0.8013 (mp10) REVERT: D 82 ASP cc_start: 0.8651 (m-30) cc_final: 0.8183 (m-30) REVERT: E 19 ARG cc_start: 0.9082 (ttt-90) cc_final: 0.8787 (mtp-110) REVERT: J 107 ASN cc_start: 0.8825 (p0) cc_final: 0.8550 (p0) REVERT: 1 1 ASP cc_start: 0.8395 (m-30) cc_final: 0.8117 (m-30) REVERT: 1 17 ASP cc_start: 0.8843 (p0) cc_final: 0.8263 (t0) REVERT: 1 21 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7874 (mm-30) REVERT: 1 22 LYS cc_start: 0.9175 (mmtp) cc_final: 0.8658 (tmtt) outliers start: 10 outliers final: 9 residues processed: 130 average time/residue: 0.5604 time to fit residues: 75.6568 Evaluate side-chains 129 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain 1 residue 19 VAL Chi-restraints excluded: chain 1 residue 24 VAL Chi-restraints excluded: chain 1 residue 314 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 125 GLN B 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.071419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.057040 restraints weight = 15300.320| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.72 r_work: 0.2852 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 5144 Z= 0.178 Angle : 0.735 9.707 6974 Z= 0.382 Chirality : 0.043 0.178 774 Planarity : 0.004 0.050 891 Dihedral : 4.823 53.293 763 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.57 % Allowed : 27.94 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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 are not related in a simple way. whole: -0.11 (0.33), residues: 634 helix: 2.31 (0.52), residues: 91 sheet: 0.60 (0.37), residues: 206 loop : -1.24 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 17 TYR 0.022 0.001 TYR D 49 PHE 0.016 0.001 PHE C 75 TRP 0.011 0.001 TRP B 36 HIS 0.005 0.001 HIS 1 8 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 5135) covalent geometry : angle 0.73437 ( 6955) SS BOND : bond 0.00326 ( 8) SS BOND : angle 0.88347 ( 16) hydrogen bonds : bond 0.04875 ( 180) hydrogen bonds : angle 4.48340 ( 489) link_NAG-ASN : bond 0.00285 ( 1) link_NAG-ASN : angle 0.75529 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 113 SER cc_start: 0.9302 (t) cc_final: 0.9082 (p) REVERT: 2 158 ASP cc_start: 0.8622 (m-30) cc_final: 0.8227 (m-30) REVERT: C 73 ASP cc_start: 0.8141 (t0) cc_final: 0.7708 (t0) REVERT: C 82 GLU cc_start: 0.9033 (tp30) cc_final: 0.8694 (tp30) REVERT: D 24 ARG cc_start: 0.8716 (mtp-110) cc_final: 0.8483 (ttm110) REVERT: D 42 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8138 (mp10) REVERT: D 79 GLN cc_start: 0.8853 (mt0) cc_final: 0.8290 (mm110) REVERT: D 82 ASP cc_start: 0.8737 (m-30) cc_final: 0.8527 (m-30) REVERT: J 107 ASN cc_start: 0.8844 (p0) cc_final: 0.8588 (p0) REVERT: 1 1 ASP cc_start: 0.8588 (m-30) cc_final: 0.8304 (m-30) REVERT: 1 17 ASP cc_start: 0.8875 (p0) cc_final: 0.8257 (t0) REVERT: 1 21 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7734 (mm-30) REVERT: 1 22 LYS cc_start: 0.9160 (mmtp) cc_final: 0.8587 (tmtt) outliers start: 14 outliers final: 10 residues processed: 128 average time/residue: 0.5407 time to fit residues: 71.9202 Evaluate side-chains 126 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 95 ILE Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain 1 residue 19 VAL Chi-restraints excluded: chain 1 residue 24 VAL Chi-restraints excluded: chain 1 residue 314 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.072029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.057673 restraints weight = 15342.086| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.75 r_work: 0.2891 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 5144 Z= 0.161 Angle : 0.757 11.503 6974 Z= 0.388 Chirality : 0.043 0.181 774 Planarity : 0.004 0.049 891 Dihedral : 4.745 52.671 763 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.89 % Favored : 94.95 % Rotamer: Outliers : 2.39 % Allowed : 28.31 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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 are not related in a simple way. whole: -0.13 (0.33), residues: 634 helix: 2.35 (0.53), residues: 91 sheet: 0.61 (0.37), residues: 206 loop : -1.28 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 17 TYR 0.024 0.001 TYR D 49 PHE 0.016 0.001 PHE C 75 TRP 0.012 0.001 TRP B 36 HIS 0.007 0.001 HIS 1 8 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 5135) covalent geometry : angle 0.75747 ( 6955) SS BOND : bond 0.00393 ( 8) SS BOND : angle 0.70463 ( 16) hydrogen bonds : bond 0.04501 ( 180) hydrogen bonds : angle 4.41891 ( 489) link_NAG-ASN : bond 0.00311 ( 1) link_NAG-ASN : angle 0.71262 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 113 SER cc_start: 0.9300 (t) cc_final: 0.9088 (p) REVERT: 2 158 ASP cc_start: 0.8556 (m-30) cc_final: 0.7879 (OUTLIER) REVERT: C 73 ASP cc_start: 0.8135 (t0) cc_final: 0.7682 (t0) REVERT: C 82 GLU cc_start: 0.9043 (tp30) cc_final: 0.8726 (tp30) REVERT: D 24 ARG cc_start: 0.8691 (mtp-110) cc_final: 0.8443 (ttm110) REVERT: D 42 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8148 (mm-40) REVERT: D 79 GLN cc_start: 0.8852 (mt0) cc_final: 0.8308 (mm110) REVERT: E 19 ARG cc_start: 0.9054 (ttt-90) cc_final: 0.8730 (mtp-110) REVERT: J 107 ASN cc_start: 0.8794 (p0) cc_final: 0.8516 (p0) REVERT: 1 1 ASP cc_start: 0.8534 (m-30) cc_final: 0.8287 (m-30) REVERT: 1 17 ASP cc_start: 0.8853 (p0) cc_final: 0.8289 (t0) REVERT: 1 21 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7715 (mm-30) REVERT: 1 22 LYS cc_start: 0.9142 (mmtp) cc_final: 0.8579 (tmtt) outliers start: 13 outliers final: 11 residues processed: 129 average time/residue: 0.5409 time to fit residues: 72.5073 Evaluate side-chains 128 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 95 ILE Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain 1 residue 19 VAL Chi-restraints excluded: chain 1 residue 24 VAL Chi-restraints excluded: chain 1 residue 314 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.071939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.057614 restraints weight = 15255.193| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.73 r_work: 0.2862 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 5144 Z= 0.157 Angle : 0.755 9.712 6974 Z= 0.387 Chirality : 0.044 0.180 774 Planarity : 0.004 0.053 891 Dihedral : 4.725 52.957 763 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 1.65 % Allowed : 30.15 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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 are not related in a simple way. whole: -0.12 (0.33), residues: 634 helix: 2.41 (0.54), residues: 91 sheet: 0.50 (0.36), residues: 212 loop : -1.25 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 101 TYR 0.023 0.001 TYR D 49 PHE 0.016 0.001 PHE C 75 TRP 0.012 0.001 TRP B 36 HIS 0.007 0.001 HIS 1 8 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 5135) covalent geometry : angle 0.75475 ( 6955) SS BOND : bond 0.00315 ( 8) SS BOND : angle 0.77393 ( 16) hydrogen bonds : bond 0.04282 ( 180) hydrogen bonds : angle 4.34868 ( 489) link_NAG-ASN : bond 0.00290 ( 1) link_NAG-ASN : angle 0.68104 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 113 SER cc_start: 0.9308 (t) cc_final: 0.9080 (p) REVERT: 2 158 ASP cc_start: 0.8505 (m-30) cc_final: 0.7858 (OUTLIER) REVERT: C 73 ASP cc_start: 0.8135 (t0) cc_final: 0.7686 (t0) REVERT: C 82 GLU cc_start: 0.9013 (tp30) cc_final: 0.8701 (tp30) REVERT: D 79 GLN cc_start: 0.8786 (mt0) cc_final: 0.8279 (mm110) REVERT: E 19 ARG cc_start: 0.9035 (ttt-90) cc_final: 0.8715 (mtp-110) REVERT: J 107 ASN cc_start: 0.8770 (p0) cc_final: 0.8475 (p0) REVERT: 1 1 ASP cc_start: 0.8537 (m-30) cc_final: 0.8307 (m-30) REVERT: 1 17 ASP cc_start: 0.8838 (p0) cc_final: 0.8361 (t0) REVERT: 1 21 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7702 (mm-30) REVERT: 1 22 LYS cc_start: 0.9120 (mmtp) cc_final: 0.8600 (tmtt) outliers start: 9 outliers final: 9 residues processed: 128 average time/residue: 0.5105 time to fit residues: 68.0631 Evaluate side-chains 126 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 95 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain 1 residue 19 VAL Chi-restraints excluded: chain 1 residue 24 VAL Chi-restraints excluded: chain 1 residue 314 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.072215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.057807 restraints weight = 15535.050| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.74 r_work: 0.2869 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 5144 Z= 0.153 Angle : 0.789 12.860 6974 Z= 0.395 Chirality : 0.043 0.177 774 Planarity : 0.005 0.066 891 Dihedral : 4.694 52.859 763 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.36 % Favored : 94.48 % Rotamer: Outliers : 1.84 % Allowed : 30.51 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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 are not related in a simple way. whole: -0.05 (0.33), residues: 634 helix: 2.42 (0.54), residues: 91 sheet: 0.68 (0.37), residues: 206 loop : -1.25 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 24 TYR 0.015 0.001 TYR E 32 PHE 0.016 0.001 PHE C 75 TRP 0.022 0.001 TRP B 36 HIS 0.006 0.001 HIS 1 8 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 5135) covalent geometry : angle 0.78903 ( 6955) SS BOND : bond 0.00268 ( 8) SS BOND : angle 0.79778 ( 16) hydrogen bonds : bond 0.04188 ( 180) hydrogen bonds : angle 4.34328 ( 489) link_NAG-ASN : bond 0.00291 ( 1) link_NAG-ASN : angle 0.64628 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2104.45 seconds wall clock time: 36 minutes 31.60 seconds (2191.60 seconds total)