Starting phenix.real_space_refine on Wed Sep 17 05:34:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g5i_51087/09_2025/9g5i_51087_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g5i_51087/09_2025/9g5i_51087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g5i_51087/09_2025/9g5i_51087_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g5i_51087/09_2025/9g5i_51087_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g5i_51087/09_2025/9g5i_51087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g5i_51087/09_2025/9g5i_51087.map" } resolution = 3.2 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 45 5.16 5 C 3253 2.51 5 N 938 2.21 5 O 1016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5252 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2363 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 316} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2436 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 453 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 1.73, per 1000 atoms: 0.33 Number of scatterers: 5252 At special positions: 0 Unit cell: (79.296, 85.904, 93.338, 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 45 16.00 O 1016 8.00 N 938 7.00 C 3253 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 688 " - pdb=" SG CYS A 701 " distance=2.01 Simple disulfide: pdb=" SG CYS A 783 " - pdb=" SG CYS A 794 " distance=2.06 Simple disulfide: pdb=" SG CYS A 906 " - pdb=" SG CYS A 928 " distance=2.06 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS A 995 " distance=2.01 Simple disulfide: pdb=" SG CYS A 990 " - pdb=" SG CYS A1006 " distance=2.06 Simple disulfide: pdb=" SG CYS B 688 " - pdb=" SG CYS B 701 " distance=2.02 Simple disulfide: pdb=" SG CYS B 783 " - pdb=" SG CYS B 794 " distance=2.04 Simple disulfide: pdb=" SG CYS B 906 " - pdb=" SG CYS B 928 " distance=2.07 Simple disulfide: pdb=" SG CYS B 987 " - pdb=" SG CYS B 995 " distance=2.06 Simple disulfide: pdb=" SG CYS B 990 " - pdb=" SG CYS B1006 " distance=2.05 Simple disulfide: pdb=" SG CYS B1008 " - pdb=" SG CYS B1021 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 147 " distance=2.01 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 134 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 241.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1198 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 6 sheets defined 19.1% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 697 through 705 Processing helix chain 'A' and resid 717 through 721 removed outlier: 3.668A pdb=" N LEU A 720 " --> pdb=" O GLU A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 796 Processing helix chain 'A' and resid 799 through 808 removed outlier: 3.586A pdb=" N ARG A 806 " --> pdb=" O GLU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 986 through 990 removed outlier: 3.749A pdb=" N CYS A 990 " --> pdb=" O CYS A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 705 Processing helix chain 'B' and resid 717 through 721 removed outlier: 4.224A pdb=" N LEU B 720 " --> pdb=" O GLU B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 795 Processing helix chain 'B' and resid 799 through 809 Processing helix chain 'B' and resid 895 through 899 Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'C' and resid 95 through 103 Processing helix chain 'C' and resid 108 through 122 removed outlier: 3.789A pdb=" N THR C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.575A pdb=" N ILE C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 682 through 685 Processing sheet with id=AA2, first strand: chain 'A' and resid 682 through 685 removed outlier: 5.386A pdb=" N GLY A 756 " --> pdb=" O VAL A 972 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 713 through 714 removed outlier: 3.501A pdb=" N GLU A 713 " --> pdb=" O ILE A 725 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N MET A 770 " --> pdb=" O MET A 830 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N MET A 830 " --> pdb=" O MET A 770 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR A 825 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE A 840 " --> pdb=" O THR A 825 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL A 827 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU A 862 " --> pdb=" O ILE A 959 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 682 through 685 removed outlier: 5.347A pdb=" N GLY B 756 " --> pdb=" O VAL B 972 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 970 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU B 760 " --> pdb=" O PRO B 968 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N ILE B 762 " --> pdb=" O TYR B 966 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N TYR B 966 " --> pdb=" O ILE B 762 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ASN B 764 " --> pdb=" O ILE B 964 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ILE B 964 " --> pdb=" O ASN B 764 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 713 through 714 removed outlier: 6.600A pdb=" N MET B 770 " --> pdb=" O MET B 830 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N MET B 830 " --> pdb=" O MET B 770 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS B 829 " --> pdb=" O PRO B 837 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LYS B 831 " --> pdb=" O PRO B 835 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG B 860 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE B 959 " --> pdb=" O ARG B 860 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU B 862 " --> pdb=" O ILE B 959 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 995 through 997 166 hydrogen bonds defined for protein. 438 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: 0.80 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 964 1.32 - 1.44: 1445 1.44 - 1.57: 2900 1.57 - 1.70: 0 1.70 - 1.83: 63 Bond restraints: 5372 Sorted by residual: bond pdb=" C GLY B 924 " pdb=" O GLY B 924 " ideal model delta sigma weight residual 1.243 1.204 0.038 9.30e-03 1.16e+04 1.69e+01 bond pdb=" C GLY B 844 " pdb=" O GLY B 844 " ideal model delta sigma weight residual 1.237 1.207 0.030 9.70e-03 1.06e+04 9.87e+00 bond pdb=" N ASP B1009 " pdb=" CA ASP B1009 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.17e-02 7.31e+03 9.83e+00 bond pdb=" N VAL B1013 " pdb=" CA VAL B1013 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.17e-02 7.31e+03 9.62e+00 bond pdb=" CA SER A 754 " pdb=" CB SER A 754 " ideal model delta sigma weight residual 1.529 1.480 0.049 1.64e-02 3.72e+03 8.84e+00 ... (remaining 5367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 6674 1.73 - 3.47: 535 3.47 - 5.20: 55 5.20 - 6.94: 5 6.94 - 8.67: 1 Bond angle restraints: 7270 Sorted by residual: angle pdb=" NE ARG C 136 " pdb=" CZ ARG C 136 " pdb=" NH2 ARG C 136 " ideal model delta sigma weight residual 119.20 122.73 -3.53 9.00e-01 1.23e+00 1.54e+01 angle pdb=" N PRO B 999 " pdb=" CA PRO B 999 " pdb=" C PRO B 999 " ideal model delta sigma weight residual 113.53 108.20 5.33 1.39e+00 5.18e-01 1.47e+01 angle pdb=" CA ASP B 832 " pdb=" CB ASP B 832 " pdb=" CG ASP B 832 " ideal model delta sigma weight residual 112.60 116.43 -3.83 1.00e+00 1.00e+00 1.46e+01 angle pdb=" N TRP A 913 " pdb=" CA TRP A 913 " pdb=" C TRP A 913 " ideal model delta sigma weight residual 114.75 110.17 4.58 1.26e+00 6.30e-01 1.32e+01 angle pdb=" C ASP B 832 " pdb=" N GLY B 833 " pdb=" CA GLY B 833 " ideal model delta sigma weight residual 123.30 119.52 3.78 1.06e+00 8.90e-01 1.27e+01 ... (remaining 7265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 2848 18.13 - 36.25: 201 36.25 - 54.37: 36 54.37 - 72.50: 15 72.50 - 90.62: 6 Dihedral angle restraints: 3106 sinusoidal: 1157 harmonic: 1949 Sorted by residual: dihedral pdb=" CA ILE A 805 " pdb=" C ILE A 805 " pdb=" N ARG A 806 " pdb=" CA ARG A 806 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA MET A 830 " pdb=" C MET A 830 " pdb=" N LYS A 831 " pdb=" CA LYS A 831 " ideal model delta harmonic sigma weight residual 180.00 154.55 25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CB CYS B 906 " pdb=" SG CYS B 906 " pdb=" SG CYS B 928 " pdb=" CB CYS B 928 " ideal model delta sinusoidal sigma weight residual -86.00 -44.55 -41.45 1 1.00e+01 1.00e-02 2.40e+01 ... (remaining 3103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 381 0.051 - 0.103: 255 0.103 - 0.154: 86 0.154 - 0.206: 21 0.206 - 0.257: 10 Chirality restraints: 753 Sorted by residual: chirality pdb=" CA PRO C 109 " pdb=" N PRO C 109 " pdb=" C PRO C 109 " pdb=" CB PRO C 109 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ASP B 832 " pdb=" N ASP B 832 " pdb=" C ASP B 832 " pdb=" CB ASP B 832 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA VAL B 728 " pdb=" N VAL B 728 " pdb=" C VAL B 728 " pdb=" CB VAL B 728 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 750 not shown) Planarity restraints: 975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 883 " -0.032 2.00e-02 2.50e+03 3.51e-02 3.08e+01 pdb=" CG TRP A 883 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP A 883 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 883 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP A 883 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TRP A 883 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP A 883 " 0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 883 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 883 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP A 883 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 739 " 0.045 2.00e-02 2.50e+03 3.52e-02 2.48e+01 pdb=" CG TYR B 739 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR B 739 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR B 739 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B 739 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 739 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 739 " 0.068 2.00e-02 2.50e+03 pdb=" OH TYR B 739 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 123 " 0.321 9.50e-02 1.11e+02 1.45e-01 1.75e+01 pdb=" NE ARG C 123 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 123 " 0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG C 123 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG C 123 " -0.001 2.00e-02 2.50e+03 ... (remaining 972 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1274 2.79 - 3.32: 4915 3.32 - 3.84: 8979 3.84 - 4.37: 11019 4.37 - 4.90: 18136 Nonbonded interactions: 44323 Sorted by model distance: nonbonded pdb=" OG SER B 895 " pdb=" OE1 GLU B 898 " model vdw 2.262 3.040 nonbonded pdb=" O VAL B 867 " pdb=" OH TYR B 937 " model vdw 2.287 3.040 nonbonded pdb=" O VAL B 972 " pdb=" NH1 ARG C 136 " model vdw 2.305 3.120 nonbonded pdb=" NH2 ARG B 753 " pdb=" OD1 ASP B 781 " model vdw 2.317 3.120 nonbonded pdb=" O PRO C 109 " pdb=" OG SER C 112 " model vdw 2.330 3.040 ... (remaining 44318 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 678 through 985 or (resid 986 and (name N or name CA or na \ me C or name O or name CB )) or resid 987 through 1008)) } 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.810 Find NCS groups from input model: 0.080 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 : 0.010 0.070 5385 Z= 0.617 Angle : 1.027 8.672 7296 Z= 0.666 Chirality : 0.075 0.257 753 Planarity : 0.009 0.145 975 Dihedral : 13.936 90.619 1869 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.27), residues: 726 helix: -1.17 (0.45), residues: 106 sheet: -1.29 (0.30), residues: 201 loop : -1.22 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.003 ARG C 123 TYR 0.068 0.009 TYR B 739 PHE 0.028 0.007 PHE C 107 TRP 0.082 0.010 TRP A 883 HIS 0.016 0.004 HIS A 983 Details of bonding type rmsd covalent geometry : bond 0.00978 ( 5372) covalent geometry : angle 1.02419 ( 7270) SS BOND : bond 0.02224 ( 13) SS BOND : angle 1.65582 ( 26) hydrogen bonds : bond 0.18941 ( 148) hydrogen bonds : angle 7.36429 ( 438) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 997 MET cc_start: 0.5168 (ttp) cc_final: 0.4519 (mtm) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0731 time to fit residues: 11.1239 Evaluate side-chains 99 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.139674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.116449 restraints weight = 9000.554| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.63 r_work: 0.3452 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5385 Z= 0.127 Angle : 0.555 8.244 7296 Z= 0.293 Chirality : 0.046 0.162 753 Planarity : 0.004 0.051 975 Dihedral : 4.715 27.778 768 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.38 % Allowed : 6.65 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.28), residues: 726 helix: 0.01 (0.49), residues: 110 sheet: -0.92 (0.31), residues: 191 loop : -1.09 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 133 TYR 0.017 0.001 TYR B 984 PHE 0.026 0.002 PHE A 685 TRP 0.008 0.001 TRP A 814 HIS 0.003 0.001 HIS A 904 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 5372) covalent geometry : angle 0.55400 ( 7270) SS BOND : bond 0.00318 ( 13) SS BOND : angle 0.83744 ( 26) hydrogen bonds : bond 0.04433 ( 148) hydrogen bonds : angle 5.59255 ( 438) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 770 MET cc_start: 0.6876 (mmm) cc_final: 0.6673 (mmt) REVERT: A 997 MET cc_start: 0.3476 (ttp) cc_final: 0.2769 (mtp) REVERT: B 947 ASP cc_start: 0.8263 (t0) cc_final: 0.8042 (t70) REVERT: C 113 LYS cc_start: 0.7737 (tppt) cc_final: 0.7522 (tppp) REVERT: C 130 TYR cc_start: 0.7931 (m-10) cc_final: 0.7558 (m-80) REVERT: C 132 LYS cc_start: 0.8331 (mmmm) cc_final: 0.8130 (mmtm) outliers start: 2 outliers final: 1 residues processed: 116 average time/residue: 0.0790 time to fit residues: 12.0489 Evaluate side-chains 99 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 985 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 23 optimal weight: 0.0040 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 777 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.143559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.119522 restraints weight = 8592.209| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.61 r_work: 0.3523 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5385 Z= 0.141 Angle : 0.533 6.282 7296 Z= 0.281 Chirality : 0.046 0.163 753 Planarity : 0.004 0.062 975 Dihedral : 4.519 26.771 768 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.33 % Allowed : 9.51 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.29), residues: 726 helix: 0.41 (0.52), residues: 109 sheet: -0.87 (0.32), residues: 190 loop : -1.02 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 123 TYR 0.010 0.001 TYR B 984 PHE 0.018 0.002 PHE A 828 TRP 0.009 0.001 TRP A 814 HIS 0.003 0.001 HIS A 904 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5372) covalent geometry : angle 0.53232 ( 7270) SS BOND : bond 0.00321 ( 13) SS BOND : angle 0.75537 ( 26) hydrogen bonds : bond 0.04037 ( 148) hydrogen bonds : angle 5.34548 ( 438) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 130 TYR cc_start: 0.8020 (m-10) cc_final: 0.7588 (m-80) outliers start: 7 outliers final: 5 residues processed: 106 average time/residue: 0.0747 time to fit residues: 10.5456 Evaluate side-chains 104 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 781 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 989 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.144220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120397 restraints weight = 8581.878| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.60 r_work: 0.3543 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5385 Z= 0.122 Angle : 0.534 10.191 7296 Z= 0.276 Chirality : 0.045 0.159 753 Planarity : 0.004 0.061 975 Dihedral : 4.386 26.832 768 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.09 % Allowed : 12.17 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.29), residues: 726 helix: 0.49 (0.52), residues: 109 sheet: -0.66 (0.34), residues: 174 loop : -1.05 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 123 TYR 0.008 0.001 TYR A 826 PHE 0.017 0.001 PHE A 828 TRP 0.008 0.001 TRP A 814 HIS 0.002 0.001 HIS A 904 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 5372) covalent geometry : angle 0.53331 ( 7270) SS BOND : bond 0.00271 ( 13) SS BOND : angle 0.60753 ( 26) hydrogen bonds : bond 0.03809 ( 148) hydrogen bonds : angle 5.20640 ( 438) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 753 ARG cc_start: 0.7101 (ptp-110) cc_final: 0.6843 (ptp-110) REVERT: A 831 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7794 (ptpt) REVERT: B 947 ASP cc_start: 0.8269 (t0) cc_final: 0.8053 (t70) REVERT: B 997 MET cc_start: 0.6549 (tpt) cc_final: 0.3633 (ptm) REVERT: C 113 LYS cc_start: 0.7941 (tppp) cc_final: 0.7606 (tppp) REVERT: C 130 TYR cc_start: 0.8011 (m-10) cc_final: 0.7630 (m-80) outliers start: 11 outliers final: 6 residues processed: 108 average time/residue: 0.0767 time to fit residues: 10.9485 Evaluate side-chains 108 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain B residue 781 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 777 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.137275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113254 restraints weight = 8886.362| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.63 r_work: 0.3435 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 5385 Z= 0.269 Angle : 0.634 7.852 7296 Z= 0.335 Chirality : 0.048 0.167 753 Planarity : 0.004 0.062 975 Dihedral : 4.927 26.648 768 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.66 % Allowed : 13.12 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.29), residues: 726 helix: 0.36 (0.51), residues: 109 sheet: -0.99 (0.31), residues: 196 loop : -1.12 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 847 TYR 0.016 0.002 TYR B 739 PHE 0.022 0.002 PHE A 828 TRP 0.014 0.002 TRP A 814 HIS 0.004 0.001 HIS A 812 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 5372) covalent geometry : angle 0.63090 ( 7270) SS BOND : bond 0.00471 ( 13) SS BOND : angle 1.22996 ( 26) hydrogen bonds : bond 0.04627 ( 148) hydrogen bonds : angle 5.56444 ( 438) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 908 GLN cc_start: 0.8341 (tp40) cc_final: 0.8130 (tp40) REVERT: B 997 MET cc_start: 0.6828 (tpt) cc_final: 0.3758 (ptm) REVERT: C 113 LYS cc_start: 0.8026 (tppp) cc_final: 0.7669 (tppp) REVERT: C 130 TYR cc_start: 0.8248 (m-10) cc_final: 0.7956 (m-80) outliers start: 14 outliers final: 12 residues processed: 113 average time/residue: 0.0690 time to fit residues: 10.6621 Evaluate side-chains 111 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 1006 CYS Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 906 CYS Chi-restraints excluded: chain B residue 972 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 989 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 ASN B 777 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.140297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.116253 restraints weight = 8883.436| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.63 r_work: 0.3479 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 : 0.003 0.035 5385 Z= 0.163 Angle : 0.568 6.721 7296 Z= 0.298 Chirality : 0.046 0.168 753 Planarity : 0.004 0.064 975 Dihedral : 4.699 26.762 768 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.28 % Allowed : 15.59 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.29), residues: 726 helix: 0.42 (0.52), residues: 109 sheet: -0.97 (0.32), residues: 189 loop : -1.12 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 847 TYR 0.011 0.001 TYR B 739 PHE 0.034 0.002 PHE C 97 TRP 0.013 0.001 TRP A 814 HIS 0.003 0.001 HIS A 812 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 5372) covalent geometry : angle 0.56591 ( 7270) SS BOND : bond 0.00332 ( 13) SS BOND : angle 1.05246 ( 26) hydrogen bonds : bond 0.03989 ( 148) hydrogen bonds : angle 5.31688 ( 438) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 868 LEU cc_start: 0.8407 (tt) cc_final: 0.8128 (mp) REVERT: A 910 MET cc_start: 0.8187 (ttm) cc_final: 0.7939 (tpt) REVERT: B 908 GLN cc_start: 0.8314 (tp40) cc_final: 0.8048 (tp40) REVERT: B 947 ASP cc_start: 0.8259 (t0) cc_final: 0.8015 (t70) REVERT: B 997 MET cc_start: 0.6655 (tpt) cc_final: 0.3641 (ptm) REVERT: C 113 LYS cc_start: 0.7975 (tppp) cc_final: 0.7696 (tppp) REVERT: C 130 TYR cc_start: 0.8200 (m-10) cc_final: 0.7890 (m-80) outliers start: 12 outliers final: 10 residues processed: 113 average time/residue: 0.0680 time to fit residues: 10.4169 Evaluate side-chains 113 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 1006 CYS Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain B residue 972 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 989 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.141741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.117857 restraints weight = 8763.671| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.62 r_work: 0.3505 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5385 Z= 0.132 Angle : 0.545 7.104 7296 Z= 0.284 Chirality : 0.046 0.171 753 Planarity : 0.004 0.062 975 Dihedral : 4.516 27.018 768 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.66 % Allowed : 15.02 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.29), residues: 726 helix: 0.43 (0.51), residues: 109 sheet: -0.86 (0.32), residues: 189 loop : -1.09 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 847 TYR 0.010 0.001 TYR B 739 PHE 0.033 0.002 PHE C 97 TRP 0.012 0.001 TRP A 814 HIS 0.003 0.001 HIS B 983 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5372) covalent geometry : angle 0.54348 ( 7270) SS BOND : bond 0.00256 ( 13) SS BOND : angle 0.84188 ( 26) hydrogen bonds : bond 0.03791 ( 148) hydrogen bonds : angle 5.21751 ( 438) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 753 ARG cc_start: 0.7073 (ptp-110) cc_final: 0.6858 (ptp-110) REVERT: A 831 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7714 (ptpt) REVERT: A 868 LEU cc_start: 0.8360 (tt) cc_final: 0.8097 (mp) REVERT: A 947 ASP cc_start: 0.8253 (t0) cc_final: 0.8049 (t0) REVERT: B 908 GLN cc_start: 0.8300 (tp40) cc_final: 0.8018 (tp40) REVERT: B 947 ASP cc_start: 0.8246 (t0) cc_final: 0.7996 (t70) REVERT: B 997 MET cc_start: 0.6611 (tpt) cc_final: 0.3702 (ptm) REVERT: C 113 LYS cc_start: 0.7919 (tppp) cc_final: 0.7678 (tppp) REVERT: C 130 TYR cc_start: 0.8127 (m-10) cc_final: 0.7809 (m-80) outliers start: 14 outliers final: 10 residues processed: 117 average time/residue: 0.0765 time to fit residues: 11.7782 Evaluate side-chains 118 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 906 CYS Chi-restraints excluded: chain B residue 972 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.140505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.116780 restraints weight = 8745.656| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.59 r_work: 0.3490 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5385 Z= 0.158 Angle : 0.570 7.644 7296 Z= 0.298 Chirality : 0.046 0.162 753 Planarity : 0.004 0.062 975 Dihedral : 4.542 27.096 768 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.66 % Allowed : 15.02 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.30), residues: 726 helix: 0.24 (0.50), residues: 109 sheet: -0.86 (0.32), residues: 189 loop : -1.08 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 847 TYR 0.011 0.001 TYR B 739 PHE 0.045 0.002 PHE C 97 TRP 0.013 0.001 TRP A 814 HIS 0.002 0.001 HIS A 812 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 5372) covalent geometry : angle 0.56843 ( 7270) SS BOND : bond 0.00283 ( 13) SS BOND : angle 0.94466 ( 26) hydrogen bonds : bond 0.03897 ( 148) hydrogen bonds : angle 5.22240 ( 438) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 753 ARG cc_start: 0.7081 (ptp-110) cc_final: 0.6846 (ptp-110) REVERT: A 868 LEU cc_start: 0.8383 (tt) cc_final: 0.8109 (mp) REVERT: A 947 ASP cc_start: 0.8311 (t0) cc_final: 0.8094 (t0) REVERT: B 908 GLN cc_start: 0.8289 (tp40) cc_final: 0.7996 (tp40) REVERT: B 947 ASP cc_start: 0.8256 (t0) cc_final: 0.8008 (t70) REVERT: B 997 MET cc_start: 0.6625 (tpt) cc_final: 0.3660 (ptm) REVERT: C 113 LYS cc_start: 0.7921 (tppp) cc_final: 0.7664 (tppp) REVERT: C 130 TYR cc_start: 0.8135 (m-10) cc_final: 0.7812 (m-80) outliers start: 14 outliers final: 13 residues processed: 109 average time/residue: 0.0807 time to fit residues: 11.6002 Evaluate side-chains 113 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 1006 CYS Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 864 ASN Chi-restraints excluded: chain B residue 906 CYS Chi-restraints excluded: chain B residue 972 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.139705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.116099 restraints weight = 8746.566| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.57 r_work: 0.3480 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5385 Z= 0.172 Angle : 0.573 7.692 7296 Z= 0.302 Chirality : 0.047 0.181 753 Planarity : 0.004 0.062 975 Dihedral : 4.624 27.258 768 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.66 % Allowed : 15.02 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.29), residues: 726 helix: 0.16 (0.50), residues: 109 sheet: -0.92 (0.33), residues: 187 loop : -1.10 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 847 TYR 0.012 0.001 TYR B 739 PHE 0.036 0.002 PHE C 97 TRP 0.014 0.001 TRP A 814 HIS 0.003 0.001 HIS A 812 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5372) covalent geometry : angle 0.57146 ( 7270) SS BOND : bond 0.00302 ( 13) SS BOND : angle 0.95927 ( 26) hydrogen bonds : bond 0.03955 ( 148) hydrogen bonds : angle 5.30953 ( 438) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 753 ARG cc_start: 0.7139 (ptp-110) cc_final: 0.6902 (ptp-110) REVERT: A 831 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7667 (ptpt) REVERT: A 868 LEU cc_start: 0.8352 (tt) cc_final: 0.8079 (mp) REVERT: A 947 ASP cc_start: 0.8348 (t0) cc_final: 0.8127 (t0) REVERT: B 908 GLN cc_start: 0.8313 (tp40) cc_final: 0.8008 (tp40) REVERT: B 947 ASP cc_start: 0.8281 (t0) cc_final: 0.8037 (t70) REVERT: C 106 TYR cc_start: 0.6869 (t80) cc_final: 0.6608 (t80) REVERT: C 113 LYS cc_start: 0.7942 (tppp) cc_final: 0.7675 (tppp) REVERT: C 130 TYR cc_start: 0.8164 (m-10) cc_final: 0.7823 (m-80) outliers start: 14 outliers final: 13 residues processed: 116 average time/residue: 0.0812 time to fit residues: 12.2540 Evaluate side-chains 115 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 1006 CYS Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 864 ASN Chi-restraints excluded: chain B residue 906 CYS Chi-restraints excluded: chain B residue 972 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 27 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.139090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.115459 restraints weight = 8899.998| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.59 r_work: 0.3470 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5385 Z= 0.185 Angle : 0.601 9.606 7296 Z= 0.314 Chirality : 0.047 0.193 753 Planarity : 0.004 0.062 975 Dihedral : 4.736 27.477 768 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.04 % Allowed : 15.02 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.35 (0.30), residues: 726 helix: 0.10 (0.51), residues: 109 sheet: -0.97 (0.34), residues: 177 loop : -1.11 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 847 TYR 0.012 0.002 TYR B 739 PHE 0.034 0.002 PHE C 97 TRP 0.016 0.002 TRP A 814 HIS 0.003 0.001 HIS A 812 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 5372) covalent geometry : angle 0.59825 ( 7270) SS BOND : bond 0.00333 ( 13) SS BOND : angle 1.09301 ( 26) hydrogen bonds : bond 0.04065 ( 148) hydrogen bonds : angle 5.34447 ( 438) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 831 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7647 (ptpt) REVERT: A 868 LEU cc_start: 0.8368 (tt) cc_final: 0.8100 (mp) REVERT: B 908 GLN cc_start: 0.8320 (tp40) cc_final: 0.8019 (tp40) REVERT: C 106 TYR cc_start: 0.6853 (t80) cc_final: 0.6586 (t80) REVERT: C 113 LYS cc_start: 0.7934 (tppp) cc_final: 0.7664 (tppp) REVERT: C 130 TYR cc_start: 0.8167 (m-10) cc_final: 0.7827 (m-80) outliers start: 16 outliers final: 15 residues processed: 110 average time/residue: 0.0651 time to fit residues: 9.8974 Evaluate side-chains 118 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 951 ASP Chi-restraints excluded: chain A residue 1006 CYS Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 781 ASP Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 864 ASN Chi-restraints excluded: chain B residue 906 CYS Chi-restraints excluded: chain B residue 972 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.141035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.117245 restraints weight = 8886.579| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.62 r_work: 0.3492 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5385 Z= 0.149 Angle : 0.591 8.428 7296 Z= 0.311 Chirality : 0.046 0.192 753 Planarity : 0.004 0.062 975 Dihedral : 4.651 27.648 768 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.85 % Allowed : 15.78 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.29), residues: 726 helix: 0.21 (0.51), residues: 109 sheet: -0.68 (0.36), residues: 161 loop : -1.20 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 847 TYR 0.010 0.001 TYR B 739 PHE 0.018 0.002 PHE A 828 TRP 0.015 0.001 TRP A 814 HIS 0.002 0.001 HIS A 812 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5372) covalent geometry : angle 0.58891 ( 7270) SS BOND : bond 0.00276 ( 13) SS BOND : angle 0.99681 ( 26) hydrogen bonds : bond 0.03865 ( 148) hydrogen bonds : angle 5.30418 ( 438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1380.68 seconds wall clock time: 24 minutes 27.63 seconds (1467.63 seconds total)