Starting phenix.real_space_refine on Tue Mar 3 13:10:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p2q_13172/03_2026/7p2q_13172_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p2q_13172/03_2026/7p2q_13172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p2q_13172/03_2026/7p2q_13172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p2q_13172/03_2026/7p2q_13172.map" model { file = "/net/cci-nas-00/data/ceres_data/7p2q_13172/03_2026/7p2q_13172_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p2q_13172/03_2026/7p2q_13172_neut.cif" } resolution = 4.9 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= 0.002 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 23 5.16 5 C 3106 2.51 5 N 778 2.21 5 O 873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 4780 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 6, 'TRANS': 141} Chain: "B" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1426 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "C" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1411 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "D" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 696 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.07, per 1000 atoms: 0.22 Number of scatterers: 4780 At special positions: 0 Unit cell: (81.81, 84.24, 126.36, 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 23 16.00 O 873 8.00 N 778 7.00 C 3106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG E 1 " - " ASN B 141 " Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 202.5 milliseconds 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1102 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 6 sheets defined 41.4% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 26 through 56 removed outlier: 4.288A pdb=" N LEU A 30 " --> pdb=" O ASN A 26 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.782A pdb=" N VAL A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 33 Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 79 through 105 Processing helix chain 'C' and resid 106 through 109 removed outlier: 3.516A pdb=" N GLU C 109 " --> pdb=" O PRO C 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 106 through 109' Processing helix chain 'C' and resid 110 through 136 removed outlier: 3.720A pdb=" N LEU C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 135 " --> pdb=" O TYR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 207 through 224 removed outlier: 3.700A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 73 removed outlier: 3.653A pdb=" N LEU D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 109 Processing helix chain 'D' and resid 112 through 131 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 140 through 145 removed outlier: 3.601A pdb=" N LEU D 145 " --> pdb=" O PRO D 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 3.983A pdb=" N ASP A 77 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 99 removed outlier: 5.282A pdb=" N VAL A 110 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS A 126 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 112 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.094A pdb=" N VAL B 51 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 63 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP B 53 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER B 61 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 129 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.679A pdb=" N GLN B 84 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 104 Processing sheet with id=AA6, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.622A pdb=" N LEU C 159 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL C 142 " --> pdb=" O TRP C 157 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TRP C 157 " --> pdb=" O VAL C 142 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 693 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: 0.56 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1460 1.34 - 1.46: 971 1.46 - 1.58: 2424 1.58 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 4896 Sorted by residual: bond pdb=" C1 BMA E 3 " pdb=" C2 BMA E 3 " ideal model delta sigma weight residual 1.519 1.567 -0.048 2.00e-02 2.50e+03 5.76e+00 bond pdb=" C1 MAN E 4 " pdb=" C2 MAN E 4 " ideal model delta sigma weight residual 1.526 1.563 -0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" C1 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sigma weight residual 1.410 1.445 -0.035 2.00e-02 2.50e+03 2.99e+00 bond pdb=" C5 MAN E 4 " pdb=" O5 MAN E 4 " ideal model delta sigma weight residual 1.418 1.452 -0.034 2.00e-02 2.50e+03 2.94e+00 bond pdb=" C LEU D 131 " pdb=" N PRO D 132 " ideal model delta sigma weight residual 1.329 1.349 -0.020 1.18e-02 7.18e+03 2.88e+00 ... (remaining 4891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 6412 1.91 - 3.81: 165 3.81 - 5.72: 31 5.72 - 7.63: 15 7.63 - 9.53: 6 Bond angle restraints: 6629 Sorted by residual: angle pdb=" C LYS B 121 " pdb=" N ASP B 122 " pdb=" CA ASP B 122 " ideal model delta sigma weight residual 121.54 131.00 -9.46 1.91e+00 2.74e-01 2.45e+01 angle pdb=" C GLY B 133 " pdb=" N ASN B 134 " pdb=" CA ASN B 134 " ideal model delta sigma weight residual 121.54 130.70 -9.16 1.91e+00 2.74e-01 2.30e+01 angle pdb=" C GLU A 58 " pdb=" N SER A 59 " pdb=" CA SER A 59 " ideal model delta sigma weight residual 121.80 130.19 -8.39 2.44e+00 1.68e-01 1.18e+01 angle pdb=" N SER A 59 " pdb=" CA SER A 59 " pdb=" C SER A 59 " ideal model delta sigma weight residual 109.81 116.82 -7.01 2.21e+00 2.05e-01 1.00e+01 angle pdb=" CA LEU D 75 " pdb=" CB LEU D 75 " pdb=" CG LEU D 75 " ideal model delta sigma weight residual 116.30 125.83 -9.53 3.50e+00 8.16e-02 7.42e+00 ... (remaining 6624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.22: 2892 21.22 - 42.44: 61 42.44 - 63.66: 4 63.66 - 84.89: 7 84.89 - 106.11: 4 Dihedral angle restraints: 2968 sinusoidal: 1260 harmonic: 1708 Sorted by residual: dihedral pdb=" CA ASP C 154 " pdb=" C ASP C 154 " pdb=" N ASP C 155 " pdb=" CA ASP C 155 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA TYR B 174 " pdb=" C TYR B 174 " pdb=" N GLU B 175 " pdb=" CA GLU B 175 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" O4 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C5 BMA E 3 " pdb=" O5 BMA E 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.40 106.11 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 2965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 590 0.057 - 0.114: 138 0.114 - 0.171: 22 0.171 - 0.228: 5 0.228 - 0.285: 1 Chirality restraints: 756 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB ILE B 109 " pdb=" CA ILE B 109 " pdb=" CG1 ILE B 109 " pdb=" CG2 ILE B 109 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASN B 134 " pdb=" N ASN B 134 " pdb=" C ASN B 134 " pdb=" CB ASN B 134 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 753 not shown) Planarity restraints: 822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 140 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO D 141 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 70 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 71 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 37 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 38 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 38 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 38 " -0.026 5.00e-02 4.00e+02 ... (remaining 819 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1005 2.79 - 3.32: 4108 3.32 - 3.85: 7306 3.85 - 4.37: 7850 4.37 - 4.90: 13680 Nonbonded interactions: 33949 Sorted by model distance: nonbonded pdb=" NH1 ARG A 109 " pdb=" CE1 PHE B 86 " model vdw 2.264 3.420 nonbonded pdb=" O LYS B 121 " pdb=" OD1 ASP B 122 " model vdw 2.290 3.040 nonbonded pdb=" NH1 ARG C 84 " pdb=" OE2 GLU C 136 " model vdw 2.352 3.120 nonbonded pdb=" OG SER B 90 " pdb=" O THR B 145 " model vdw 2.357 3.040 nonbonded pdb=" OD1 ASP A 120 " pdb=" NZ LYS A 147 " model vdw 2.401 3.120 ... (remaining 33944 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 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: 0.430 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: 0.080 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.980 Find NCS groups from input model: 0.020 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 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 0.048 4901 Z= 0.211 Angle : 0.853 9.532 6644 Z= 0.434 Chirality : 0.051 0.285 756 Planarity : 0.007 0.057 821 Dihedral : 11.107 106.107 1866 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: -3.09 (0.29), residues: 579 helix: -1.26 (0.24), residues: 220 sheet: -1.18 (0.47), residues: 120 loop : -3.26 (0.32), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 112 TYR 0.023 0.002 TYR B 174 PHE 0.024 0.002 PHE A 80 TRP 0.017 0.002 TRP C 157 HIS 0.009 0.002 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 4896) covalent geometry : angle 0.83964 ( 6629) hydrogen bonds : bond 0.11371 ( 241) hydrogen bonds : angle 6.54284 ( 693) link_ALPHA1-3 : bond 0.00522 ( 1) link_ALPHA1-3 : angle 1.87116 ( 3) link_ALPHA1-6 : bond 0.00239 ( 1) link_ALPHA1-6 : angle 1.44688 ( 3) link_BETA1-4 : bond 0.01835 ( 2) link_BETA1-4 : angle 4.60829 ( 6) link_NAG-ASN : bond 0.00215 ( 1) link_NAG-ASN : angle 2.51512 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8490 (m-10) cc_final: 0.7728 (m-80) REVERT: A 52 ILE cc_start: 0.8925 (pt) cc_final: 0.8577 (pt) REVERT: A 90 ARG cc_start: 0.7608 (mtm110) cc_final: 0.7111 (mmt90) REVERT: A 134 ASP cc_start: 0.8211 (m-30) cc_final: 0.7241 (t0) REVERT: A 146 GLU cc_start: 0.6990 (tt0) cc_final: 0.6721 (tt0) REVERT: A 158 LEU cc_start: 0.8953 (mm) cc_final: 0.8745 (mm) REVERT: B 42 HIS cc_start: 0.8714 (m-70) cc_final: 0.8398 (t-170) REVERT: B 49 LYS cc_start: 0.8171 (ptmt) cc_final: 0.7917 (ptpp) REVERT: B 59 GLU cc_start: 0.7296 (tp30) cc_final: 0.6951 (tp30) REVERT: B 73 ASP cc_start: 0.8255 (t0) cc_final: 0.7368 (t70) REVERT: B 78 PHE cc_start: 0.7880 (m-80) cc_final: 0.7514 (m-80) REVERT: B 80 TRP cc_start: 0.6359 (m100) cc_final: 0.5855 (p-90) REVERT: B 128 PHE cc_start: 0.7994 (m-10) cc_final: 0.7751 (m-10) REVERT: C 70 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8536 (tm-30) REVERT: C 102 ASP cc_start: 0.8659 (m-30) cc_final: 0.8314 (m-30) REVERT: C 174 LEU cc_start: 0.8449 (mm) cc_final: 0.7492 (mm) REVERT: C 208 TYR cc_start: 0.9119 (t80) cc_final: 0.8689 (t80) REVERT: D 68 MET cc_start: 0.9152 (mtt) cc_final: 0.8798 (tmm) REVERT: D 128 LEU cc_start: 0.8645 (mt) cc_final: 0.8394 (pp) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.0846 time to fit residues: 27.4055 Evaluate side-chains 150 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.2980 chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.078552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.062386 restraints weight = 28654.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.064055 restraints weight = 22246.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.065320 restraints weight = 18191.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.066328 restraints weight = 15454.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.066925 restraints weight = 13561.566| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4901 Z= 0.160 Angle : 0.719 8.128 6644 Z= 0.366 Chirality : 0.046 0.224 756 Planarity : 0.006 0.066 821 Dihedral : 10.600 86.170 731 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.19 % Allowed : 1.34 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.33), residues: 579 helix: 0.72 (0.32), residues: 220 sheet: -0.87 (0.48), residues: 126 loop : -2.78 (0.34), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 145 TYR 0.021 0.002 TYR D 117 PHE 0.018 0.002 PHE A 37 TRP 0.018 0.002 TRP C 101 HIS 0.009 0.002 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 4896) covalent geometry : angle 0.70839 ( 6629) hydrogen bonds : bond 0.03839 ( 241) hydrogen bonds : angle 5.30107 ( 693) link_ALPHA1-3 : bond 0.00769 ( 1) link_ALPHA1-3 : angle 1.32784 ( 3) link_ALPHA1-6 : bond 0.00200 ( 1) link_ALPHA1-6 : angle 2.13885 ( 3) link_BETA1-4 : bond 0.01219 ( 2) link_BETA1-4 : angle 3.62662 ( 6) link_NAG-ASN : bond 0.00037 ( 1) link_NAG-ASN : angle 1.98668 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.8970 (m-80) cc_final: 0.8637 (m-80) REVERT: A 32 TYR cc_start: 0.8091 (m-10) cc_final: 0.7736 (m-80) REVERT: A 33 GLN cc_start: 0.8989 (mm110) cc_final: 0.8602 (mm-40) REVERT: A 36 ASN cc_start: 0.9149 (m110) cc_final: 0.8922 (m110) REVERT: A 46 MET cc_start: 0.7839 (ttp) cc_final: 0.7633 (ttp) REVERT: A 51 LEU cc_start: 0.9495 (mt) cc_final: 0.9289 (mt) REVERT: A 121 ILE cc_start: 0.6674 (mm) cc_final: 0.5881 (mm) REVERT: A 134 ASP cc_start: 0.7507 (m-30) cc_final: 0.7137 (t0) REVERT: A 146 GLU cc_start: 0.6840 (tt0) cc_final: 0.6577 (tt0) REVERT: A 158 LEU cc_start: 0.9117 (mm) cc_final: 0.8493 (mm) REVERT: B 42 HIS cc_start: 0.8727 (m-70) cc_final: 0.8438 (t-170) REVERT: B 73 ASP cc_start: 0.8379 (t0) cc_final: 0.7015 (t70) REVERT: B 80 TRP cc_start: 0.6463 (m100) cc_final: 0.5580 (p-90) REVERT: B 122 ASP cc_start: 0.8730 (p0) cc_final: 0.8529 (p0) REVERT: B 131 ASP cc_start: 0.6044 (t0) cc_final: 0.5805 (t0) REVERT: C 70 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8547 (tm-30) REVERT: C 102 ASP cc_start: 0.8568 (m-30) cc_final: 0.8303 (m-30) REVERT: C 208 TYR cc_start: 0.9046 (t80) cc_final: 0.8762 (t80) REVERT: D 131 LEU cc_start: 0.8912 (mt) cc_final: 0.8474 (mt) REVERT: D 139 ARG cc_start: 0.8377 (ttt180) cc_final: 0.8031 (ptt180) outliers start: 1 outliers final: 1 residues processed: 188 average time/residue: 0.0816 time to fit residues: 18.9621 Evaluate side-chains 134 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 49 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 143 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.073726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057080 restraints weight = 27534.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.058550 restraints weight = 21434.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.059699 restraints weight = 17676.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.060586 restraints weight = 15148.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.061308 restraints weight = 13391.308| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4901 Z= 0.187 Angle : 0.744 8.901 6644 Z= 0.379 Chirality : 0.046 0.183 756 Planarity : 0.005 0.049 821 Dihedral : 9.699 75.821 731 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.80 % Favored : 96.03 % Rotamer: Outliers : 0.19 % Allowed : 3.84 % Favored : 95.97 % 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: -0.80 (0.34), residues: 579 helix: 1.19 (0.33), residues: 226 sheet: -0.02 (0.51), residues: 118 loop : -2.64 (0.35), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 165 TYR 0.022 0.002 TYR D 117 PHE 0.016 0.002 PHE A 37 TRP 0.023 0.002 TRP B 148 HIS 0.005 0.002 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 4896) covalent geometry : angle 0.73639 ( 6629) hydrogen bonds : bond 0.04011 ( 241) hydrogen bonds : angle 5.22670 ( 693) link_ALPHA1-3 : bond 0.00910 ( 1) link_ALPHA1-3 : angle 1.63088 ( 3) link_ALPHA1-6 : bond 0.00319 ( 1) link_ALPHA1-6 : angle 2.03988 ( 3) link_BETA1-4 : bond 0.01049 ( 2) link_BETA1-4 : angle 2.98474 ( 6) link_NAG-ASN : bond 0.00127 ( 1) link_NAG-ASN : angle 2.05160 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.9011 (m-80) cc_final: 0.8638 (m-80) REVERT: A 32 TYR cc_start: 0.8101 (m-10) cc_final: 0.7764 (m-80) REVERT: A 33 GLN cc_start: 0.9131 (mm110) cc_final: 0.8710 (mm110) REVERT: A 36 ASN cc_start: 0.8998 (m110) cc_final: 0.8753 (m110) REVERT: A 46 MET cc_start: 0.7952 (ttp) cc_final: 0.7248 (ttp) REVERT: A 133 ASP cc_start: 0.7008 (t70) cc_final: 0.6563 (t0) REVERT: A 134 ASP cc_start: 0.7716 (m-30) cc_final: 0.7145 (t0) REVERT: A 146 GLU cc_start: 0.6843 (tt0) cc_final: 0.6546 (tt0) REVERT: B 42 HIS cc_start: 0.8783 (m-70) cc_final: 0.8538 (m-70) REVERT: B 122 ASP cc_start: 0.8781 (p0) cc_final: 0.8552 (p0) REVERT: C 70 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8592 (tm-30) REVERT: C 71 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8673 (tppt) REVERT: C 94 PHE cc_start: 0.8797 (m-10) cc_final: 0.8481 (m-10) REVERT: C 121 TYR cc_start: 0.8097 (t80) cc_final: 0.7742 (t80) REVERT: C 208 TYR cc_start: 0.8982 (t80) cc_final: 0.8712 (t80) REVERT: D 129 LEU cc_start: 0.8920 (mt) cc_final: 0.8511 (mt) outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.0658 time to fit residues: 14.7085 Evaluate side-chains 128 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 33 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN B 50 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.073836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.057407 restraints weight = 26903.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.058992 restraints weight = 20616.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.060182 restraints weight = 16782.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.061072 restraints weight = 14276.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.061794 restraints weight = 12558.948| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4901 Z= 0.145 Angle : 0.700 10.595 6644 Z= 0.349 Chirality : 0.045 0.183 756 Planarity : 0.004 0.045 821 Dihedral : 8.965 66.730 731 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: -0.58 (0.35), residues: 579 helix: 1.41 (0.34), residues: 226 sheet: -0.11 (0.51), residues: 126 loop : -2.50 (0.36), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 109 TYR 0.018 0.002 TYR B 88 PHE 0.016 0.002 PHE A 37 TRP 0.014 0.001 TRP B 148 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4896) covalent geometry : angle 0.69151 ( 6629) hydrogen bonds : bond 0.03757 ( 241) hydrogen bonds : angle 4.95787 ( 693) link_ALPHA1-3 : bond 0.00790 ( 1) link_ALPHA1-3 : angle 1.71646 ( 3) link_ALPHA1-6 : bond 0.00380 ( 1) link_ALPHA1-6 : angle 2.06751 ( 3) link_BETA1-4 : bond 0.01295 ( 2) link_BETA1-4 : angle 2.99791 ( 6) link_NAG-ASN : bond 0.00110 ( 1) link_NAG-ASN : angle 2.01642 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9593 (mt) cc_final: 0.9393 (mt) REVERT: A 111 ILE cc_start: 0.9154 (tp) cc_final: 0.8930 (tp) REVERT: A 112 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8531 (mmmt) REVERT: A 146 GLU cc_start: 0.6599 (tt0) cc_final: 0.6233 (tt0) REVERT: A 158 LEU cc_start: 0.9226 (mm) cc_final: 0.8689 (mm) REVERT: B 42 HIS cc_start: 0.8785 (m-70) cc_final: 0.8530 (m-70) REVERT: B 49 LYS cc_start: 0.6885 (mttm) cc_final: 0.6661 (mptt) REVERT: B 122 ASP cc_start: 0.8760 (p0) cc_final: 0.8543 (p0) REVERT: C 70 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8525 (tm-30) REVERT: C 102 ASP cc_start: 0.8560 (m-30) cc_final: 0.8311 (m-30) REVERT: C 124 MET cc_start: 0.8039 (ppp) cc_final: 0.7636 (ptt) REVERT: C 188 GLU cc_start: 0.8922 (pp20) cc_final: 0.8672 (pp20) REVERT: C 208 TYR cc_start: 0.9029 (t80) cc_final: 0.8730 (t80) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.0666 time to fit residues: 14.2763 Evaluate side-chains 132 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 41 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.072741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.056905 restraints weight = 28167.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.058339 restraints weight = 21856.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.059441 restraints weight = 17973.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.060286 restraints weight = 15438.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.060962 restraints weight = 13647.609| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4901 Z= 0.153 Angle : 0.716 7.894 6644 Z= 0.359 Chirality : 0.045 0.189 756 Planarity : 0.004 0.045 821 Dihedral : 8.496 59.743 731 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: -0.49 (0.35), residues: 579 helix: 1.45 (0.34), residues: 222 sheet: 0.18 (0.52), residues: 119 loop : -2.44 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 109 TYR 0.031 0.002 TYR A 32 PHE 0.023 0.002 PHE C 94 TRP 0.015 0.001 TRP D 134 HIS 0.003 0.001 HIS D 71 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4896) covalent geometry : angle 0.70807 ( 6629) hydrogen bonds : bond 0.03748 ( 241) hydrogen bonds : angle 5.00706 ( 693) link_ALPHA1-3 : bond 0.00867 ( 1) link_ALPHA1-3 : angle 1.85033 ( 3) link_ALPHA1-6 : bond 0.00194 ( 1) link_ALPHA1-6 : angle 1.93375 ( 3) link_BETA1-4 : bond 0.01094 ( 2) link_BETA1-4 : angle 2.95291 ( 6) link_NAG-ASN : bond 0.00170 ( 1) link_NAG-ASN : angle 2.11338 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.8978 (m-80) cc_final: 0.8663 (m-80) REVERT: A 32 TYR cc_start: 0.7992 (m-80) cc_final: 0.7624 (m-80) REVERT: A 33 GLN cc_start: 0.9128 (mm110) cc_final: 0.8711 (mm110) REVERT: A 112 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8570 (mmmt) REVERT: A 146 GLU cc_start: 0.6620 (tt0) cc_final: 0.6190 (tt0) REVERT: B 42 HIS cc_start: 0.8724 (m-70) cc_final: 0.8474 (m-70) REVERT: B 47 MET cc_start: 0.6741 (tmm) cc_final: 0.6494 (tmm) REVERT: B 80 TRP cc_start: 0.6790 (m100) cc_final: 0.6286 (p-90) REVERT: B 87 LEU cc_start: 0.9005 (tp) cc_final: 0.8778 (tp) REVERT: B 122 ASP cc_start: 0.8808 (p0) cc_final: 0.8584 (p0) REVERT: C 70 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8285 (tm-30) REVERT: C 71 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8154 (mmmt) REVERT: C 102 ASP cc_start: 0.8584 (m-30) cc_final: 0.8345 (m-30) REVERT: C 124 MET cc_start: 0.7896 (ppp) cc_final: 0.7361 (ptt) REVERT: C 188 GLU cc_start: 0.8965 (pp20) cc_final: 0.8707 (pp20) REVERT: C 208 TYR cc_start: 0.9045 (t80) cc_final: 0.8758 (t80) REVERT: D 71 HIS cc_start: 0.7295 (m90) cc_final: 0.7025 (m170) REVERT: D 139 ARG cc_start: 0.8464 (ttt180) cc_final: 0.8151 (ptt180) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.0748 time to fit residues: 15.5752 Evaluate side-chains 128 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 53 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 40 optimal weight: 0.0970 chunk 29 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN C 58 ASN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.068639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.054005 restraints weight = 30404.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.055306 restraints weight = 23764.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.056268 restraints weight = 19597.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.057055 restraints weight = 16883.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.057552 restraints weight = 14966.214| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4901 Z= 0.226 Angle : 0.817 12.096 6644 Z= 0.414 Chirality : 0.048 0.202 756 Planarity : 0.005 0.046 821 Dihedral : 8.198 58.686 731 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: -0.95 (0.34), residues: 579 helix: 1.09 (0.34), residues: 221 sheet: -0.42 (0.52), residues: 118 loop : -2.48 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 109 TYR 0.025 0.002 TYR A 32 PHE 0.017 0.003 PHE A 84 TRP 0.008 0.001 TRP B 80 HIS 0.006 0.002 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 4896) covalent geometry : angle 0.80904 ( 6629) hydrogen bonds : bond 0.04370 ( 241) hydrogen bonds : angle 5.29501 ( 693) link_ALPHA1-3 : bond 0.00530 ( 1) link_ALPHA1-3 : angle 2.29681 ( 3) link_ALPHA1-6 : bond 0.00152 ( 1) link_ALPHA1-6 : angle 2.10050 ( 3) link_BETA1-4 : bond 0.01126 ( 2) link_BETA1-4 : angle 3.05497 ( 6) link_NAG-ASN : bond 0.00273 ( 1) link_NAG-ASN : angle 2.29321 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8062 (m-80) cc_final: 0.7694 (m-80) REVERT: A 33 GLN cc_start: 0.9130 (mm110) cc_final: 0.8724 (mm110) REVERT: A 69 MET cc_start: 0.9507 (mmm) cc_final: 0.9286 (mmm) REVERT: A 128 ASP cc_start: 0.8860 (t0) cc_final: 0.8566 (t0) REVERT: A 146 GLU cc_start: 0.6747 (tt0) cc_final: 0.6386 (tt0) REVERT: A 158 LEU cc_start: 0.9322 (mm) cc_final: 0.8854 (mm) REVERT: B 42 HIS cc_start: 0.8753 (m-70) cc_final: 0.8457 (m90) REVERT: B 49 LYS cc_start: 0.7245 (mttt) cc_final: 0.6932 (mttp) REVERT: B 122 ASP cc_start: 0.8879 (p0) cc_final: 0.8644 (p0) REVERT: C 70 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8308 (tm-30) REVERT: C 71 LYS cc_start: 0.8947 (mmmm) cc_final: 0.8477 (tppt) REVERT: C 102 ASP cc_start: 0.8694 (m-30) cc_final: 0.8408 (m-30) REVERT: C 124 MET cc_start: 0.7971 (ppp) cc_final: 0.7475 (ptm) REVERT: C 188 GLU cc_start: 0.9046 (pp20) cc_final: 0.8676 (pp20) REVERT: D 71 HIS cc_start: 0.7354 (m90) cc_final: 0.7043 (m-70) REVERT: D 134 TRP cc_start: 0.6978 (m100) cc_final: 0.6743 (m100) REVERT: D 139 ARG cc_start: 0.8561 (ttt180) cc_final: 0.8238 (ptt180) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0751 time to fit residues: 14.7135 Evaluate side-chains 124 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.070450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.055230 restraints weight = 27952.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.056668 restraints weight = 21468.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057795 restraints weight = 17498.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.058595 restraints weight = 14865.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.059320 restraints weight = 13137.608| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.7227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4901 Z= 0.138 Angle : 0.742 10.645 6644 Z= 0.366 Chirality : 0.045 0.153 756 Planarity : 0.004 0.038 821 Dihedral : 6.955 55.578 731 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: -0.71 (0.34), residues: 579 helix: 1.35 (0.34), residues: 221 sheet: -0.28 (0.49), residues: 119 loop : -2.42 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 145 TYR 0.020 0.001 TYR B 88 PHE 0.015 0.002 PHE A 37 TRP 0.009 0.001 TRP D 134 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4896) covalent geometry : angle 0.73276 ( 6629) hydrogen bonds : bond 0.03945 ( 241) hydrogen bonds : angle 5.06824 ( 693) link_ALPHA1-3 : bond 0.00757 ( 1) link_ALPHA1-3 : angle 1.82661 ( 3) link_ALPHA1-6 : bond 0.00114 ( 1) link_ALPHA1-6 : angle 1.96360 ( 3) link_BETA1-4 : bond 0.01242 ( 2) link_BETA1-4 : angle 3.18091 ( 6) link_NAG-ASN : bond 0.00137 ( 1) link_NAG-ASN : angle 2.20090 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8126 (m-80) cc_final: 0.7768 (m-80) REVERT: A 33 GLN cc_start: 0.9116 (mm110) cc_final: 0.8692 (mm110) REVERT: A 46 MET cc_start: 0.7979 (ttp) cc_final: 0.7388 (ttp) REVERT: A 93 GLU cc_start: 0.6049 (pm20) cc_final: 0.5595 (pm20) REVERT: A 112 LYS cc_start: 0.9115 (mmmt) cc_final: 0.8664 (mmmt) REVERT: A 146 GLU cc_start: 0.6788 (tt0) cc_final: 0.6269 (tt0) REVERT: B 42 HIS cc_start: 0.8686 (m-70) cc_final: 0.8447 (m-70) REVERT: B 49 LYS cc_start: 0.7172 (mttt) cc_final: 0.6956 (mttp) REVERT: B 122 ASP cc_start: 0.8862 (p0) cc_final: 0.8610 (p0) REVERT: C 70 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8600 (tm-30) REVERT: C 102 ASP cc_start: 0.8604 (m-30) cc_final: 0.8294 (m-30) REVERT: C 124 MET cc_start: 0.7806 (ppp) cc_final: 0.7482 (ptt) REVERT: C 166 PHE cc_start: 0.6457 (m-10) cc_final: 0.5558 (m-10) REVERT: C 174 LEU cc_start: 0.9139 (mp) cc_final: 0.8901 (mp) REVERT: C 188 GLU cc_start: 0.9007 (pp20) cc_final: 0.8669 (pp20) REVERT: C 208 TYR cc_start: 0.8995 (t80) cc_final: 0.8704 (t80) REVERT: D 71 HIS cc_start: 0.7435 (m90) cc_final: 0.7176 (m-70) REVERT: D 139 ARG cc_start: 0.8507 (ttt180) cc_final: 0.8205 (ptt180) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.0693 time to fit residues: 14.2215 Evaluate side-chains 125 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.068955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.054643 restraints weight = 29892.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055946 restraints weight = 23308.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.056960 restraints weight = 19246.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.057618 restraints weight = 16496.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.058350 restraints weight = 14694.918| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.7444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4901 Z= 0.183 Angle : 0.767 10.703 6644 Z= 0.382 Chirality : 0.045 0.145 756 Planarity : 0.004 0.036 821 Dihedral : 6.524 54.902 731 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -0.76 (0.34), residues: 579 helix: 1.25 (0.34), residues: 221 sheet: -0.13 (0.48), residues: 122 loop : -2.52 (0.35), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 28 TYR 0.015 0.002 TYR B 88 PHE 0.015 0.002 PHE A 37 TRP 0.009 0.001 TRP D 134 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 4896) covalent geometry : angle 0.75913 ( 6629) hydrogen bonds : bond 0.04056 ( 241) hydrogen bonds : angle 5.05308 ( 693) link_ALPHA1-3 : bond 0.00562 ( 1) link_ALPHA1-3 : angle 1.83859 ( 3) link_ALPHA1-6 : bond 0.00494 ( 1) link_ALPHA1-6 : angle 2.21553 ( 3) link_BETA1-4 : bond 0.01030 ( 2) link_BETA1-4 : angle 2.94298 ( 6) link_NAG-ASN : bond 0.00106 ( 1) link_NAG-ASN : angle 2.18230 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLN cc_start: 0.9132 (mm110) cc_final: 0.8692 (mm110) REVERT: A 69 MET cc_start: 0.9523 (mmm) cc_final: 0.9291 (mmm) REVERT: A 77 ASP cc_start: 0.7750 (m-30) cc_final: 0.7294 (t70) REVERT: A 80 PHE cc_start: 0.7745 (p90) cc_final: 0.7463 (p90) REVERT: A 93 GLU cc_start: 0.5757 (pm20) cc_final: 0.5551 (pm20) REVERT: A 112 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8654 (mmmt) REVERT: A 128 ASP cc_start: 0.8771 (t0) cc_final: 0.8461 (t70) REVERT: A 146 GLU cc_start: 0.6760 (tt0) cc_final: 0.6251 (tt0) REVERT: A 158 LEU cc_start: 0.9424 (mm) cc_final: 0.8785 (mm) REVERT: B 42 HIS cc_start: 0.8712 (m-70) cc_final: 0.8450 (m90) REVERT: B 47 MET cc_start: 0.6869 (tmm) cc_final: 0.6664 (tmm) REVERT: B 49 LYS cc_start: 0.7125 (mttt) cc_final: 0.6918 (mttp) REVERT: B 122 ASP cc_start: 0.8857 (p0) cc_final: 0.8605 (p0) REVERT: C 70 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8324 (tm-30) REVERT: C 71 LYS cc_start: 0.8929 (mmmm) cc_final: 0.8556 (tppt) REVERT: C 96 ILE cc_start: 0.9465 (mm) cc_final: 0.9106 (tp) REVERT: C 97 VAL cc_start: 0.9455 (p) cc_final: 0.9239 (m) REVERT: C 102 ASP cc_start: 0.8604 (m-30) cc_final: 0.8297 (m-30) REVERT: C 124 MET cc_start: 0.7769 (ppp) cc_final: 0.7377 (ptm) REVERT: C 166 PHE cc_start: 0.6473 (m-10) cc_final: 0.5513 (m-10) REVERT: C 188 GLU cc_start: 0.9037 (pp20) cc_final: 0.8692 (pp20) REVERT: D 71 HIS cc_start: 0.7379 (m90) cc_final: 0.7135 (m-70) REVERT: D 139 ARG cc_start: 0.8560 (ttt180) cc_final: 0.8264 (ptt180) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.0704 time to fit residues: 14.0998 Evaluate side-chains 125 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 34 optimal weight: 0.0970 chunk 7 optimal weight: 0.0470 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 0.0060 chunk 3 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.071830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.057215 restraints weight = 28556.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.058702 restraints weight = 21892.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.059837 restraints weight = 17808.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.060742 restraints weight = 15107.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.061456 restraints weight = 13175.408| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.7442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4901 Z= 0.132 Angle : 0.770 11.098 6644 Z= 0.376 Chirality : 0.046 0.167 756 Planarity : 0.004 0.035 821 Dihedral : 6.108 56.476 731 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: -0.80 (0.34), residues: 579 helix: 1.15 (0.34), residues: 221 sheet: -0.16 (0.47), residues: 127 loop : -2.51 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 28 TYR 0.014 0.001 TYR C 121 PHE 0.015 0.002 PHE C 197 TRP 0.012 0.001 TRP C 157 HIS 0.003 0.001 HIS C 199 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4896) covalent geometry : angle 0.76324 ( 6629) hydrogen bonds : bond 0.03850 ( 241) hydrogen bonds : angle 4.77139 ( 693) link_ALPHA1-3 : bond 0.00833 ( 1) link_ALPHA1-3 : angle 1.14809 ( 3) link_ALPHA1-6 : bond 0.00227 ( 1) link_ALPHA1-6 : angle 1.74508 ( 3) link_BETA1-4 : bond 0.01179 ( 2) link_BETA1-4 : angle 2.97036 ( 6) link_NAG-ASN : bond 0.00135 ( 1) link_NAG-ASN : angle 2.01881 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8246 (m-80) cc_final: 0.7956 (m-80) REVERT: A 33 GLN cc_start: 0.9105 (mm110) cc_final: 0.8655 (mm110) REVERT: A 93 GLU cc_start: 0.5909 (pm20) cc_final: 0.5674 (pm20) REVERT: A 112 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8642 (mmmt) REVERT: A 121 ILE cc_start: 0.6915 (mm) cc_final: 0.6683 (mm) REVERT: A 146 GLU cc_start: 0.6503 (tt0) cc_final: 0.6000 (tt0) REVERT: A 158 LEU cc_start: 0.9337 (mm) cc_final: 0.8826 (mm) REVERT: A 163 MET cc_start: 0.8532 (mtm) cc_final: 0.8219 (mpp) REVERT: B 42 HIS cc_start: 0.8706 (m-70) cc_final: 0.8463 (m90) REVERT: B 49 LYS cc_start: 0.7158 (mttt) cc_final: 0.6878 (mttp) REVERT: B 122 ASP cc_start: 0.8921 (p0) cc_final: 0.8655 (p0) REVERT: B 127 TYR cc_start: 0.8425 (t80) cc_final: 0.8132 (t80) REVERT: C 70 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8446 (tm-30) REVERT: C 71 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8552 (mmtt) REVERT: C 96 ILE cc_start: 0.9436 (mm) cc_final: 0.9086 (tp) REVERT: C 102 ASP cc_start: 0.8479 (m-30) cc_final: 0.8144 (m-30) REVERT: C 166 PHE cc_start: 0.6401 (m-10) cc_final: 0.5742 (m-10) REVERT: C 188 GLU cc_start: 0.8976 (pp20) cc_final: 0.8688 (pp20) REVERT: D 71 HIS cc_start: 0.7529 (m90) cc_final: 0.7275 (m-70) REVERT: D 82 LYS cc_start: 0.8140 (mptt) cc_final: 0.7350 (mmmt) REVERT: D 85 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8629 (mmtt) REVERT: D 129 LEU cc_start: 0.8916 (mt) cc_final: 0.8678 (mp) REVERT: D 134 TRP cc_start: 0.7232 (m100) cc_final: 0.6907 (m100) REVERT: D 139 ARG cc_start: 0.8464 (ttt180) cc_final: 0.8138 (ptt180) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.0686 time to fit residues: 14.2922 Evaluate side-chains 128 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.069965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055717 restraints weight = 29225.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.057186 restraints weight = 22448.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.058304 restraints weight = 18214.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.059170 restraints weight = 15431.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.059804 restraints weight = 13471.440| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.7912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4901 Z= 0.155 Angle : 0.784 10.981 6644 Z= 0.389 Chirality : 0.045 0.148 756 Planarity : 0.004 0.042 821 Dihedral : 6.214 55.708 731 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.79 (0.34), residues: 579 helix: 1.14 (0.35), residues: 221 sheet: 0.34 (0.51), residues: 106 loop : -2.56 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 138 TYR 0.030 0.002 TYR D 81 PHE 0.012 0.002 PHE A 37 TRP 0.033 0.002 TRP B 148 HIS 0.004 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 4896) covalent geometry : angle 0.77759 ( 6629) hydrogen bonds : bond 0.03956 ( 241) hydrogen bonds : angle 4.89143 ( 693) link_ALPHA1-3 : bond 0.00602 ( 1) link_ALPHA1-3 : angle 1.47042 ( 3) link_ALPHA1-6 : bond 0.00231 ( 1) link_ALPHA1-6 : angle 1.99404 ( 3) link_BETA1-4 : bond 0.01011 ( 2) link_BETA1-4 : angle 2.73097 ( 6) link_NAG-ASN : bond 0.00007 ( 1) link_NAG-ASN : angle 2.03965 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8195 (m-80) cc_final: 0.7985 (m-80) REVERT: A 112 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8639 (mmmt) REVERT: A 121 ILE cc_start: 0.6838 (mm) cc_final: 0.6620 (mm) REVERT: A 146 GLU cc_start: 0.6544 (tt0) cc_final: 0.5902 (tt0) REVERT: B 42 HIS cc_start: 0.8659 (m-70) cc_final: 0.8409 (m90) REVERT: B 49 LYS cc_start: 0.7127 (mttt) cc_final: 0.6918 (mttp) REVERT: B 122 ASP cc_start: 0.8914 (p0) cc_final: 0.8650 (p0) REVERT: C 96 ILE cc_start: 0.9479 (mm) cc_final: 0.9114 (tp) REVERT: C 97 VAL cc_start: 0.9427 (p) cc_final: 0.9212 (m) REVERT: C 102 ASP cc_start: 0.8490 (m-30) cc_final: 0.8155 (m-30) REVERT: C 188 GLU cc_start: 0.9004 (pp20) cc_final: 0.8727 (pp20) REVERT: D 71 HIS cc_start: 0.7479 (m90) cc_final: 0.7241 (m-70) REVERT: D 128 LEU cc_start: 0.8894 (tt) cc_final: 0.8680 (pp) REVERT: D 139 ARG cc_start: 0.8542 (ttt180) cc_final: 0.8242 (ptt180) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.0680 time to fit residues: 13.1732 Evaluate side-chains 121 residues out of total 521 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.071182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.056996 restraints weight = 29338.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.058414 restraints weight = 22512.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.059541 restraints weight = 18331.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.060402 restraints weight = 15545.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.061064 restraints weight = 13575.550| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.7949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4901 Z= 0.133 Angle : 0.772 11.103 6644 Z= 0.382 Chirality : 0.046 0.204 756 Planarity : 0.004 0.034 821 Dihedral : 6.134 56.271 731 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.75 (0.35), residues: 579 helix: 1.26 (0.35), residues: 221 sheet: -0.07 (0.50), residues: 111 loop : -2.45 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 145 TYR 0.027 0.001 TYR D 81 PHE 0.030 0.002 PHE C 197 TRP 0.031 0.002 TRP B 148 HIS 0.004 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4896) covalent geometry : angle 0.76549 ( 6629) hydrogen bonds : bond 0.03872 ( 241) hydrogen bonds : angle 4.80254 ( 693) link_ALPHA1-3 : bond 0.00650 ( 1) link_ALPHA1-3 : angle 1.35097 ( 3) link_ALPHA1-6 : bond 0.00040 ( 1) link_ALPHA1-6 : angle 1.75729 ( 3) link_BETA1-4 : bond 0.01025 ( 2) link_BETA1-4 : angle 2.74105 ( 6) link_NAG-ASN : bond 0.00156 ( 1) link_NAG-ASN : angle 1.92200 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 923.16 seconds wall clock time: 16 minutes 37.40 seconds (997.40 seconds total)