Starting phenix.real_space_refine on Tue Aug 4 15:49:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z18_73732/08_2026/9z18_73732.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z18_73732/08_2026/9z18_73732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z18_73732/08_2026/9z18_73732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z18_73732/08_2026/9z18_73732.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z18_73732/08_2026/9z18_73732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z18_73732/08_2026/9z18_73732.map" } resolution = 2.9 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= 0.007 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 24 5.16 5 C 2816 2.51 5 N 745 2.21 5 O 865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4450 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 952 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 865 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 103} Chain: "A" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2619 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 17, 'TRANS': 325} Chain breaks: 1 Chain: "A" 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 Time building chain proxies: 0.98, per 1000 atoms: 0.22 Number of scatterers: 4450 At special positions: 0 Unit cell: (89.3, 59.22, 107.16, 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 24 16.00 O 865 8.00 N 745 7.00 C 2816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 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 A1301 " - " ASN A 801 " Time building additional restraints: 0.20 Conformation dependent library (CDL) restraints added in 103.3 milliseconds 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1064 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 8 sheets defined 41.6% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.662A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 749 through 783 removed outlier: 5.441A pdb=" N SER A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE A 759 " --> pdb=" O GLN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 removed outlier: 3.572A pdb=" N PHE A 800 " --> pdb=" O PHE A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.875A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 832 through 842 removed outlier: 3.641A pdb=" N CYS A 840 " --> pdb=" O GLN A 836 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 841 " --> pdb=" O TYR A 837 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 842 " --> pdb=" O GLY A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 846 No H-bonds generated for 'chain 'A' and resid 844 through 846' Processing helix chain 'A' and resid 847 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.690A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.651A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.686A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.997A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.512A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.715A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.504A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA7, first strand: chain 'A' and resid 720 through 728 removed outlier: 5.829A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 734 through 736 260 hydrogen bonds defined for protein. 714 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: 0.44 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1442 1.34 - 1.46: 1031 1.46 - 1.58: 2032 1.58 - 1.70: 0 1.70 - 1.82: 35 Bond restraints: 4540 Sorted by residual: bond pdb=" N LYS A 921 " pdb=" CA LYS A 921 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.80e+00 bond pdb=" N THR A 719 " pdb=" CA THR A 719 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" C GLU L 17 " pdb=" N PRO L 18 " ideal model delta sigma weight residual 1.332 1.353 -0.021 1.26e-02 6.30e+03 2.80e+00 ... (remaining 4535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 5678 0.99 - 1.99: 384 1.99 - 2.98: 66 2.98 - 3.98: 27 3.98 - 4.97: 10 Bond angle restraints: 6165 Sorted by residual: angle pdb=" C GLU L 17 " pdb=" N PRO L 18 " pdb=" CA PRO L 18 " ideal model delta sigma weight residual 119.92 122.62 -2.70 1.07e+00 8.73e-01 6.38e+00 angle pdb=" C GLU L 17 " pdb=" CA GLU L 17 " pdb=" CB GLU L 17 " ideal model delta sigma weight residual 109.26 112.60 -3.34 1.47e+00 4.63e-01 5.17e+00 angle pdb=" C ARG A 815 " pdb=" CA ARG A 815 " pdb=" CB ARG A 815 " ideal model delta sigma weight residual 109.94 114.62 -4.68 2.13e+00 2.20e-01 4.83e+00 angle pdb=" CA LYS A 921 " pdb=" C LYS A 921 " pdb=" O LYS A 921 " ideal model delta sigma weight residual 120.42 118.15 2.27 1.06e+00 8.90e-01 4.59e+00 angle pdb=" CA TRP H 100A" pdb=" CB TRP H 100A" pdb=" CG TRP H 100A" ideal model delta sigma weight residual 113.60 117.52 -3.92 1.90e+00 2.77e-01 4.25e+00 ... (remaining 6160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 2463 17.51 - 35.01: 205 35.01 - 52.52: 64 52.52 - 70.03: 14 70.03 - 87.54: 8 Dihedral angle restraints: 2754 sinusoidal: 1089 harmonic: 1665 Sorted by residual: dihedral pdb=" CA CYS A1032 " pdb=" C CYS A1032 " pdb=" N VAL A1033 " pdb=" CA VAL A1033 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA SER L 52 " pdb=" C SER L 52 " pdb=" N ASN L 53 " pdb=" CA ASN L 53 " ideal model delta harmonic sigma weight residual -180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual 93.00 53.01 39.99 1 1.00e+01 1.00e-02 2.25e+01 ... (remaining 2751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 539 0.044 - 0.088: 118 0.088 - 0.131: 41 0.131 - 0.175: 3 0.175 - 0.219: 1 Chirality restraints: 702 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE H 69 " pdb=" CA ILE H 69 " pdb=" CG1 ILE H 69 " pdb=" CG2 ILE H 69 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 699 not shown) Planarity restraints: 797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 801 " -0.021 2.00e-02 2.50e+03 1.94e-02 4.71e+00 pdb=" CG ASN A 801 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 801 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 801 " 0.024 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 935 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C GLN A 935 " -0.032 2.00e-02 2.50e+03 pdb=" O GLN A 935 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP A 936 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 820 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C ASP A 820 " -0.028 2.00e-02 2.50e+03 pdb=" O ASP A 820 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 821 " 0.010 2.00e-02 2.50e+03 ... (remaining 794 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1603 2.87 - 3.38: 4355 3.38 - 3.88: 7309 3.88 - 4.39: 8732 4.39 - 4.90: 14576 Nonbonded interactions: 36575 Sorted by model distance: nonbonded pdb=" OD2 ASP H 53 " pdb=" OG SER H 55 " model vdw 2.360 3.040 nonbonded pdb=" O MET A1029 " pdb=" O VAL A1033 " model vdw 2.498 3.040 nonbonded pdb=" OD1 ASN A 914 " pdb=" N VAL A 915 " model vdw 2.521 3.120 nonbonded pdb=" ND1 HIS L 27D" pdb=" OD1 ASN L 28 " model vdw 2.528 3.120 nonbonded pdb=" O GLY A 880 " pdb=" O SER A 884 " model vdw 2.560 3.040 ... (remaining 36570 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: 8.830 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: 0.010 Set scattering table: 0.010 Process input model: 4.290 Find NCS groups from input model: 0.010 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:5.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.003 0.034 4547 Z= 0.155 Angle : 0.631 8.745 6180 Z= 0.339 Chirality : 0.042 0.219 702 Planarity : 0.006 0.058 796 Dihedral : 15.526 87.536 1672 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.41 % Allowed : 17.44 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -0.25 (0.34), residues: 569 helix: -0.45 (0.31), residues: 202 sheet: 0.39 (0.43), residues: 128 loop : 0.01 (0.42), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.003 ARG L 77 TYR 0.014 0.002 TYR L 87 PHE 0.019 0.002 PHE A 759 TRP 0.020 0.002 TRP H 100A HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 ( 4540) covalent geometry : angle 0.61383 / 0.33 ( 6165) SS BOND : bond 0.00428 / 0.21 ( 6) SS BOND : angle 1.82797 / 1.12 ( 12) hydrogen bonds : bond 0.16208 / 11.06 ( 248) hydrogen bonds : angle 7.76264 / 5.34 ( 714) link_NAG-ASN : bond 0.00421 / 0.22 ( 1) link_NAG-ASN : angle 5.78872 / 3.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: L 4 MET cc_start: 0.7170 (mpp) cc_final: 0.6714 (mpp) REVERT: L 33 LEU cc_start: 0.7240 (tt) cc_final: 0.7014 (tp) REVERT: L 37 LEU cc_start: 0.8320 (tm) cc_final: 0.8079 (tp) REVERT: A 825 LYS cc_start: 0.7838 (mtpp) cc_final: 0.7481 (ttmm) REVERT: A 1006 THR cc_start: 0.7990 (m) cc_final: 0.7762 (m) REVERT: A 1028 LYS cc_start: 0.8069 (ttmt) cc_final: 0.7821 (ttmt) outliers start: 2 outliers final: 2 residues processed: 108 average time/residue: 0.3714 time to fit residues: 41.8133 Evaluate side-chains 104 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 102 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 56 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.0170 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 overall best weight: 0.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 28 ASN A 755 GLN A 774 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.142118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.127645 restraints weight = 6086.738| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.67 r_work: 0.3479 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4547 Z= 0.174 Angle : 0.621 6.475 6180 Z= 0.329 Chirality : 0.043 0.143 702 Planarity : 0.005 0.051 796 Dihedral : 6.454 45.349 649 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.43 % Allowed : 16.43 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.39 (0.34), residues: 569 helix: 0.61 (0.34), residues: 201 sheet: 0.49 (0.43), residues: 126 loop : 0.00 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 61 TYR 0.016 0.002 TYR L 49 PHE 0.019 0.002 PHE H 29 TRP 0.017 0.002 TRP H 100A HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 4540) covalent geometry : angle 0.61372 / 0.33 ( 6165) SS BOND : bond 0.00518 / 0.26 ( 6) SS BOND : angle 1.97091 / 1.18 ( 12) hydrogen bonds : bond 0.04429 / 3.06 ( 248) hydrogen bonds : angle 5.68044 / 3.88 ( 714) link_NAG-ASN : bond 0.00363 / 0.19 ( 1) link_NAG-ASN : angle 2.44569 / 1.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: L 4 MET cc_start: 0.6951 (mpp) cc_final: 0.6698 (mpp) REVERT: L 72 THR cc_start: 0.8087 (p) cc_final: 0.7801 (m) REVERT: A 815 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.5658 (ptp90) REVERT: A 961 THR cc_start: 0.7829 (t) cc_final: 0.7463 (p) REVERT: A 1028 LYS cc_start: 0.7995 (ttmt) cc_final: 0.7753 (ttmt) outliers start: 12 outliers final: 7 residues processed: 114 average time/residue: 0.3782 time to fit residues: 44.9640 Evaluate side-chains 110 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 922 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 0.0770 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.0970 chunk 48 optimal weight: 0.4980 chunk 26 optimal weight: 0.0670 chunk 2 optimal weight: 0.0770 chunk 1 optimal weight: 0.0370 chunk 35 optimal weight: 0.9990 overall best weight: 0.0710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN A 755 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.144115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129805 restraints weight = 6026.095| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.68 r_work: 0.3504 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4547 Z= 0.112 Angle : 0.548 5.859 6180 Z= 0.287 Chirality : 0.041 0.143 702 Planarity : 0.004 0.041 796 Dihedral : 5.791 44.596 644 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.43 % Allowed : 18.26 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.60 (0.34), residues: 569 helix: 0.86 (0.35), residues: 201 sheet: 0.66 (0.43), residues: 126 loop : -0.00 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.017 0.001 TYR L 49 PHE 0.013 0.001 PHE H 29 TRP 0.014 0.001 TRP H 100A HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 4540) covalent geometry : angle 0.54308 / 0.29 ( 6165) SS BOND : bond 0.00398 / 0.20 ( 6) SS BOND : angle 1.43000 / 0.88 ( 12) hydrogen bonds : bond 0.03882 / 2.68 ( 248) hydrogen bonds : angle 5.27816 / 3.61 ( 714) link_NAG-ASN : bond 0.00576 / 0.30 ( 1) link_NAG-ASN : angle 2.00237 / 1.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.153 Fit side-chains revert: symmetry clash REVERT: H 7 SER cc_start: 0.8246 (OUTLIER) cc_final: 0.8023 (p) REVERT: L 4 MET cc_start: 0.6974 (mpp) cc_final: 0.6691 (mpp) REVERT: A 773 GLU cc_start: 0.7669 (tt0) cc_final: 0.7334 (tt0) REVERT: A 869 MET cc_start: 0.7908 (mtp) cc_final: 0.7545 (mtp) REVERT: A 959 LEU cc_start: 0.7954 (mp) cc_final: 0.7704 (mp) REVERT: A 961 THR cc_start: 0.7760 (t) cc_final: 0.7360 (p) REVERT: A 1028 LYS cc_start: 0.7912 (ttmt) cc_final: 0.7620 (mttt) outliers start: 12 outliers final: 8 residues processed: 102 average time/residue: 0.3809 time to fit residues: 40.6237 Evaluate side-chains 102 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 922 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 17 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 16 optimal weight: 0.0970 chunk 29 optimal weight: 0.0020 chunk 19 optimal weight: 0.0980 overall best weight: 0.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 774 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.145070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130467 restraints weight = 5962.988| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.73 r_work: 0.3521 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4547 Z= 0.109 Angle : 0.532 7.087 6180 Z= 0.275 Chirality : 0.040 0.144 702 Planarity : 0.004 0.059 796 Dihedral : 5.425 43.446 644 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.84 % Allowed : 17.85 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.78 (0.35), residues: 569 helix: 1.09 (0.35), residues: 199 sheet: 0.65 (0.43), residues: 130 loop : 0.09 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.012 0.001 TYR H 91 PHE 0.011 0.001 PHE L 98 TRP 0.013 0.001 TRP H 100A HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 4540) covalent geometry : angle 0.52761 / 0.27 ( 6165) SS BOND : bond 0.00388 / 0.20 ( 6) SS BOND : angle 1.36568 / 0.84 ( 12) hydrogen bonds : bond 0.03705 / 2.54 ( 248) hydrogen bonds : angle 5.01243 / 3.42 ( 714) link_NAG-ASN : bond 0.00568 / 0.30 ( 1) link_NAG-ASN : angle 1.79578 / 1.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: H 7 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.8055 (p) REVERT: L 4 MET cc_start: 0.7018 (mpp) cc_final: 0.6714 (mpp) REVERT: A 725 GLU cc_start: 0.7411 (tt0) cc_final: 0.7046 (tt0) REVERT: A 764 ASN cc_start: 0.7937 (t0) cc_final: 0.7612 (t0) REVERT: A 773 GLU cc_start: 0.7611 (tt0) cc_final: 0.7343 (tt0) REVERT: A 815 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.5562 (ptp90) REVERT: A 825 LYS cc_start: 0.7193 (mtpp) cc_final: 0.6911 (mttp) REVERT: A 869 MET cc_start: 0.7975 (mtp) cc_final: 0.7625 (mtp) REVERT: A 961 THR cc_start: 0.7664 (t) cc_final: 0.7258 (p) REVERT: A 1028 LYS cc_start: 0.7797 (ttmt) cc_final: 0.7483 (mttt) outliers start: 14 outliers final: 7 residues processed: 108 average time/residue: 0.3616 time to fit residues: 40.8547 Evaluate side-chains 104 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 864 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 49 optimal weight: 0.2980 chunk 4 optimal weight: 0.0970 chunk 40 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 0.0770 chunk 9 optimal weight: 0.0980 overall best weight: 0.1736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 774 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.143373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.128801 restraints weight = 6020.735| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.69 r_work: 0.3492 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4547 Z= 0.143 Angle : 0.546 5.825 6180 Z= 0.284 Chirality : 0.041 0.136 702 Planarity : 0.005 0.053 796 Dihedral : 5.479 43.246 644 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.04 % Allowed : 19.07 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.81 (0.35), residues: 569 helix: 1.09 (0.35), residues: 199 sheet: 0.62 (0.44), residues: 130 loop : 0.16 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.014 0.002 TYR A1007 PHE 0.014 0.002 PHE H 29 TRP 0.012 0.001 TRP H 100A HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4540) covalent geometry : angle 0.54190 / 0.28 ( 6165) SS BOND : bond 0.00486 / 0.25 ( 6) SS BOND : angle 1.45487 / 0.86 ( 12) hydrogen bonds : bond 0.03868 / 2.67 ( 248) hydrogen bonds : angle 5.06514 / 3.46 ( 714) link_NAG-ASN : bond 0.00497 / 0.26 ( 1) link_NAG-ASN : angle 1.80099 / 1.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: H 7 SER cc_start: 0.8290 (m) cc_final: 0.8050 (p) REVERT: L 4 MET cc_start: 0.7013 (mpp) cc_final: 0.6715 (mpp) REVERT: A 725 GLU cc_start: 0.7508 (tt0) cc_final: 0.6972 (tt0) REVERT: A 773 GLU cc_start: 0.7712 (tt0) cc_final: 0.7404 (tt0) REVERT: A 815 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.5511 (ptp90) REVERT: A 961 THR cc_start: 0.7840 (t) cc_final: 0.7437 (p) REVERT: A 1028 LYS cc_start: 0.7840 (ttmt) cc_final: 0.7513 (mttt) outliers start: 15 outliers final: 8 residues processed: 103 average time/residue: 0.3644 time to fit residues: 39.0403 Evaluate side-chains 101 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 922 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.0370 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 31 optimal weight: 0.0770 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 27 optimal weight: 0.0970 overall best weight: 0.1172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 774 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.144211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.129650 restraints weight = 6164.699| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.72 r_work: 0.3506 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4547 Z= 0.116 Angle : 0.515 5.852 6180 Z= 0.268 Chirality : 0.040 0.139 702 Planarity : 0.004 0.053 796 Dihedral : 5.276 42.866 644 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.84 % Allowed : 19.68 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.89 (0.35), residues: 569 helix: 1.22 (0.35), residues: 199 sheet: 0.63 (0.43), residues: 130 loop : 0.18 (0.44), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.013 0.001 TYR H 91 PHE 0.011 0.001 PHE L 98 TRP 0.013 0.001 TRP H 100A HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 4540) covalent geometry : angle 0.51123 / 0.27 ( 6165) SS BOND : bond 0.00461 / 0.24 ( 6) SS BOND : angle 1.30715 / 0.80 ( 12) hydrogen bonds : bond 0.03647 / 2.50 ( 248) hydrogen bonds : angle 4.92487 / 3.35 ( 714) link_NAG-ASN : bond 0.00517 / 0.27 ( 1) link_NAG-ASN : angle 1.71107 / 0.99 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: H 7 SER cc_start: 0.8258 (m) cc_final: 0.8033 (p) REVERT: L 4 MET cc_start: 0.7117 (mpp) cc_final: 0.6789 (mpp) REVERT: A 725 GLU cc_start: 0.7506 (tt0) cc_final: 0.6952 (tt0) REVERT: A 773 GLU cc_start: 0.7660 (tt0) cc_final: 0.7370 (tt0) REVERT: A 825 LYS cc_start: 0.7060 (mtpp) cc_final: 0.6775 (mttm) REVERT: A 961 THR cc_start: 0.7815 (t) cc_final: 0.7392 (p) REVERT: A 1028 LYS cc_start: 0.7785 (ttmt) cc_final: 0.7469 (mttt) outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 0.3624 time to fit residues: 39.3244 Evaluate side-chains 102 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 931 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 28 optimal weight: 0.5980 chunk 49 optimal weight: 0.0870 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 17 optimal weight: 0.0570 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 41 optimal weight: 0.0470 chunk 50 optimal weight: 0.1980 chunk 7 optimal weight: 0.2980 chunk 30 optimal weight: 0.0670 overall best weight: 0.0912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 774 GLN ** A1048 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 = 0.3809 r_free = 0.3809 target = 0.144772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130184 restraints weight = 6138.578| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.73 r_work: 0.3515 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4547 Z= 0.107 Angle : 0.505 5.864 6180 Z= 0.262 Chirality : 0.040 0.143 702 Planarity : 0.004 0.050 796 Dihedral : 5.129 42.204 644 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.64 % Allowed : 19.88 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 1.04 (0.36), residues: 569 helix: 1.32 (0.35), residues: 199 sheet: 0.69 (0.42), residues: 137 loop : 0.28 (0.45), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.014 0.001 TYR L 87 PHE 0.011 0.001 PHE L 98 TRP 0.012 0.001 TRP H 100A HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 4540) covalent geometry : angle 0.50166 / 0.26 ( 6165) SS BOND : bond 0.00379 / 0.19 ( 6) SS BOND : angle 1.21608 / 0.75 ( 12) hydrogen bonds : bond 0.03545 / 2.42 ( 248) hydrogen bonds : angle 4.81901 / 3.27 ( 714) link_NAG-ASN : bond 0.00533 / 0.28 ( 1) link_NAG-ASN : angle 1.59875 / 0.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: H 7 SER cc_start: 0.8272 (m) cc_final: 0.8054 (p) REVERT: L 4 MET cc_start: 0.7114 (mpp) cc_final: 0.6769 (mpp) REVERT: A 725 GLU cc_start: 0.7502 (tt0) cc_final: 0.6980 (tt0) REVERT: A 773 GLU cc_start: 0.7678 (tt0) cc_final: 0.7320 (tt0) REVERT: A 825 LYS cc_start: 0.7006 (mtpp) cc_final: 0.6751 (mttp) REVERT: A 961 THR cc_start: 0.7823 (t) cc_final: 0.7378 (p) REVERT: A 1028 LYS cc_start: 0.7692 (ttmt) cc_final: 0.7407 (mttt) outliers start: 13 outliers final: 10 residues processed: 100 average time/residue: 0.3955 time to fit residues: 41.2246 Evaluate side-chains 99 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 931 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 0.0970 chunk 46 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 774 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.141658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.127122 restraints weight = 5986.077| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.67 r_work: 0.3470 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4547 Z= 0.223 Angle : 0.602 7.207 6180 Z= 0.313 Chirality : 0.043 0.133 702 Planarity : 0.005 0.050 796 Dihedral : 5.651 43.019 644 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.03 % Allowed : 21.10 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.74 (0.36), residues: 569 helix: 0.91 (0.35), residues: 199 sheet: 0.60 (0.43), residues: 137 loop : 0.24 (0.45), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 815 TYR 0.019 0.002 TYR L 87 PHE 0.017 0.002 PHE H 29 TRP 0.011 0.002 TRP H 100A HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.22 ( 4540) covalent geometry : angle 0.59573 / 0.31 ( 6165) SS BOND : bond 0.00627 / 0.32 ( 6) SS BOND : angle 1.80243 / 1.05 ( 12) hydrogen bonds : bond 0.04143 / 2.86 ( 248) hydrogen bonds : angle 5.16819 / 3.53 ( 714) link_NAG-ASN : bond 0.00284 / 0.15 ( 1) link_NAG-ASN : angle 2.04104 / 1.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.8691 (mmm) cc_final: 0.8191 (mmt) REVERT: L 4 MET cc_start: 0.7137 (mpp) cc_final: 0.6808 (mpp) REVERT: A 725 GLU cc_start: 0.7564 (tt0) cc_final: 0.7046 (tt0) REVERT: A 773 GLU cc_start: 0.7857 (tt0) cc_final: 0.7552 (tt0) REVERT: A 825 LYS cc_start: 0.7462 (mtpp) cc_final: 0.7106 (mttp) REVERT: A 961 THR cc_start: 0.7885 (t) cc_final: 0.7524 (p) REVERT: A 1028 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7624 (mttt) outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 0.3711 time to fit residues: 37.1873 Evaluate side-chains 95 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 922 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 36 optimal weight: 0.3980 chunk 35 optimal weight: 0.4980 chunk 55 optimal weight: 0.3980 chunk 54 optimal weight: 0.2980 chunk 9 optimal weight: 0.4980 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 11 optimal weight: 0.0870 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN A 755 GLN ** A1048 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 = 0.3768 r_free = 0.3768 target = 0.141535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.126989 restraints weight = 5976.718| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.68 r_work: 0.3470 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4547 Z= 0.200 Angle : 0.596 7.559 6180 Z= 0.308 Chirality : 0.043 0.199 702 Planarity : 0.005 0.074 796 Dihedral : 5.683 42.448 644 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.64 % Allowed : 20.69 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 (0.36), residues: 569 helix: 0.73 (0.35), residues: 199 sheet: 0.55 (0.43), residues: 136 loop : 0.17 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.019 0.002 TYR L 87 PHE 0.015 0.002 PHE H 29 TRP 0.012 0.002 TRP H 100A HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 4540) covalent geometry : angle 0.58966 / 0.31 ( 6165) SS BOND : bond 0.00578 / 0.30 ( 6) SS BOND : angle 1.82701 / 1.07 ( 12) hydrogen bonds : bond 0.04064 / 2.79 ( 248) hydrogen bonds : angle 5.24578 / 3.58 ( 714) link_NAG-ASN : bond 0.00293 / 0.15 ( 1) link_NAG-ASN : angle 2.02401 / 1.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.8715 (mmm) cc_final: 0.8392 (mmt) REVERT: L 4 MET cc_start: 0.7170 (mpp) cc_final: 0.6829 (mpp) REVERT: A 725 GLU cc_start: 0.7618 (tt0) cc_final: 0.7100 (tt0) REVERT: A 773 GLU cc_start: 0.7839 (tt0) cc_final: 0.7505 (tt0) REVERT: A 815 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6026 (ttp80) REVERT: A 825 LYS cc_start: 0.7542 (mtpp) cc_final: 0.7204 (mttp) REVERT: A 961 THR cc_start: 0.7882 (t) cc_final: 0.7529 (p) REVERT: A 1028 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7629 (mttt) outliers start: 13 outliers final: 9 residues processed: 98 average time/residue: 0.4102 time to fit residues: 41.8951 Evaluate side-chains 99 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1055 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.0970 chunk 37 optimal weight: 0.0570 chunk 41 optimal weight: 0.1980 chunk 13 optimal weight: 0.1980 chunk 2 optimal weight: 0.1980 chunk 34 optimal weight: 0.0770 chunk 14 optimal weight: 0.0010 overall best weight: 0.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 755 GLN ** A1048 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 = 0.3805 r_free = 0.3805 target = 0.144420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130033 restraints weight = 6018.474| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.68 r_work: 0.3511 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4547 Z= 0.109 Angle : 0.523 5.782 6180 Z= 0.270 Chirality : 0.040 0.135 702 Planarity : 0.005 0.071 796 Dihedral : 5.300 41.952 644 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.23 % Allowed : 21.70 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.81 (0.36), residues: 569 helix: 1.06 (0.35), residues: 199 sheet: 0.60 (0.43), residues: 137 loop : 0.20 (0.46), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.017 0.001 TYR L 87 PHE 0.010 0.001 PHE L 98 TRP 0.013 0.001 TRP H 100A HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 4540) covalent geometry : angle 0.51853 / 0.27 ( 6165) SS BOND : bond 0.00443 / 0.23 ( 6) SS BOND : angle 1.39131 / 0.83 ( 12) hydrogen bonds : bond 0.03632 / 2.47 ( 248) hydrogen bonds : angle 4.97667 / 3.39 ( 714) link_NAG-ASN : bond 0.00511 / 0.27 ( 1) link_NAG-ASN : angle 1.69970 / 0.97 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1138 Ramachandran restraints generated. 569 Oldfield, 0 Emsley, 569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.096 Fit side-chains revert: symmetry clash REVERT: H 7 SER cc_start: 0.8287 (m) cc_final: 0.8068 (p) REVERT: L 4 MET cc_start: 0.7147 (mpp) cc_final: 0.6780 (mpp) REVERT: A 773 GLU cc_start: 0.7788 (tt0) cc_final: 0.7504 (tt0) REVERT: A 815 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.5903 (ttp80) REVERT: A 825 LYS cc_start: 0.7296 (mtpp) cc_final: 0.7011 (mttp) REVERT: A 961 THR cc_start: 0.7850 (t) cc_final: 0.7454 (p) outliers start: 11 outliers final: 8 residues processed: 99 average time/residue: 0.3659 time to fit residues: 37.8111 Evaluate side-chains 98 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 815 ARG Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 1055 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 54 optimal weight: 0.0170 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 0.0980 chunk 16 optimal weight: 0.0870 overall best weight: 0.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 774 GLN ** A1048 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 = 0.3794 r_free = 0.3794 target = 0.143568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.128944 restraints weight = 5995.739| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.70 r_work: 0.3498 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4547 Z= 0.135 Angle : 0.537 6.284 6180 Z= 0.279 Chirality : 0.041 0.195 702 Planarity : 0.005 0.068 796 Dihedral : 5.340 41.706 644 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.83 % Allowed : 22.31 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 (0.36), residues: 569 helix: 1.06 (0.35), residues: 199 sheet: 0.63 (0.43), residues: 137 loop : 0.16 (0.46), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.018 0.002 TYR L 87 PHE 0.012 0.002 PHE H 29 TRP 0.012 0.001 TRP H 100A HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4540) covalent geometry : angle 0.53211 / 0.28 ( 6165) SS BOND : bond 0.00492 / 0.25 ( 6) SS BOND : angle 1.49922 / 0.89 ( 12) hydrogen bonds : bond 0.03733 / 2.55 ( 248) hydrogen bonds : angle 5.04955 / 3.44 ( 714) link_NAG-ASN : bond 0.00435 / 0.23 ( 1) link_NAG-ASN : angle 1.72211 / 0.98 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1590.12 seconds wall clock time: 27 minutes 50.83 seconds (1670.83 seconds total)