Starting phenix.real_space_refine on Fri Aug 22 15:34:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c07_16356/08_2025/8c07_16356.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c07_16356/08_2025/8c07_16356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8c07_16356/08_2025/8c07_16356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c07_16356/08_2025/8c07_16356.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c07_16356/08_2025/8c07_16356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c07_16356/08_2025/8c07_16356.map" } resolution = 3.3 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= 0.001 sd= 0.018 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 19 5.16 5 C 3159 2.51 5 N 875 2.21 5 O 921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4974 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3475 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 31, 'TRANS': 418} Chain breaks: 3 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 10, 'GLN:plan1': 5, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "I" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "K" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 563 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 358 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'SY8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.42, per 1000 atoms: 0.29 Number of scatterers: 4974 At special positions: 0 Unit cell: (68.9472, 90.2272, 102.995, 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 19 16.00 O 921 8.00 N 875 7.00 C 3159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of additional links: simple=1, symmetry=0 Simple link: pdb=" C GLY K 75 " - pdb=" N SY8 K 101 " Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 197.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1216 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 44.7% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'B' and resid 2026 through 2030 removed outlier: 3.629A pdb=" N MET B2029 " --> pdb=" O SER B2026 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B2030 " --> pdb=" O ASP B2027 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2026 through 2030' Processing helix chain 'B' and resid 2043 through 2048 Processing helix chain 'B' and resid 2048 through 2053 removed outlier: 4.278A pdb=" N ASP B2052 " --> pdb=" O ILE B2048 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN B2053 " --> pdb=" O PRO B2049 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2048 through 2053' Processing helix chain 'B' and resid 2063 through 2068 Processing helix chain 'B' and resid 2217 through 2236 removed outlier: 3.590A pdb=" N LYS B2221 " --> pdb=" O GLY B2217 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B2224 " --> pdb=" O VAL B2220 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B2236 " --> pdb=" O LEU B2232 " (cutoff:3.500A) Processing helix chain 'B' and resid 2248 through 2259 Processing helix chain 'B' and resid 2289 through 2305 removed outlier: 4.409A pdb=" N ARG B2293 " --> pdb=" O SER B2289 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B2305 " --> pdb=" O GLN B2301 " (cutoff:3.500A) Processing helix chain 'B' and resid 2524 through 2531 Processing helix chain 'B' and resid 2532 through 2542 removed outlier: 3.747A pdb=" N LEU B2536 " --> pdb=" O ILE B2532 " (cutoff:3.500A) Processing helix chain 'B' and resid 2551 through 2560 Processing helix chain 'B' and resid 2564 through 2571 removed outlier: 3.615A pdb=" N ALA B2569 " --> pdb=" O HIS B2566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2572 through 2586 Processing helix chain 'B' and resid 2594 through 2599 removed outlier: 3.931A pdb=" N ASP B2599 " --> pdb=" O PHE B2595 " (cutoff:3.500A) Processing helix chain 'B' and resid 2627 through 2629 No H-bonds generated for 'chain 'B' and resid 2627 through 2629' Processing helix chain 'B' and resid 2630 through 2645 removed outlier: 3.814A pdb=" N VAL B2645 " --> pdb=" O HIS B2641 " (cutoff:3.500A) Processing helix chain 'B' and resid 2647 through 2660 Processing helix chain 'B' and resid 2671 through 2681 removed outlier: 3.556A pdb=" N VAL B2679 " --> pdb=" O PHE B2675 " (cutoff:3.500A) Processing helix chain 'B' and resid 2686 through 2693 Processing helix chain 'B' and resid 2709 through 2720 removed outlier: 3.906A pdb=" N TRP B2713 " --> pdb=" O GLN B2709 " (cutoff:3.500A) Processing helix chain 'B' and resid 2722 through 2735 Processing helix chain 'B' and resid 2742 through 2746 removed outlier: 3.545A pdb=" N PHE B2746 " --> pdb=" O GLU B2743 " (cutoff:3.500A) Processing helix chain 'B' and resid 2780 through 2791 Processing helix chain 'I' and resid 22 through 33 Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'K' and resid 22 through 34 Processing helix chain 'J' and resid 186 through 197 removed outlier: 4.297A pdb=" N ILE J 190 " --> pdb=" O PRO J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 212 removed outlier: 3.868A pdb=" N ILE J 205 " --> pdb=" O SER J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 225 Processing sheet with id=AA1, first strand: chain 'B' and resid 2238 through 2243 removed outlier: 6.774A pdb=" N ARG B2238 " --> pdb=" O HIS B2275 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B2277 " --> pdb=" O ARG B2238 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B2240 " --> pdb=" O VAL B2277 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL B2279 " --> pdb=" O LEU B2240 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B2242 " --> pdb=" O VAL B2279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 2505 through 2506 Processing sheet with id=AA3, first strand: chain 'B' and resid 2603 through 2605 Processing sheet with id=AA4, first strand: chain 'B' and resid 2697 through 2698 removed outlier: 6.680A pdb=" N SER B2751 " --> pdb=" O LEU B2772 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL B2774 " --> pdb=" O SER B2751 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR B2753 " --> pdb=" O VAL B2774 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 12 through 16 removed outlier: 4.229A pdb=" N ILE I 13 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL I 5 " --> pdb=" O ILE I 13 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU I 15 " --> pdb=" O ILE I 3 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE I 3 " --> pdb=" O LEU I 15 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU I 67 " --> pdb=" O GLN I 2 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N PHE I 4 " --> pdb=" O LEU I 67 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU I 69 " --> pdb=" O PHE I 4 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS I 6 " --> pdb=" O LEU I 69 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N LEU I 71 " --> pdb=" O LYS I 6 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE I 44 " --> pdb=" O HIS I 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.842A pdb=" N LYS K 6 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU K 69 " --> pdb=" O LYS K 6 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS K 68 " --> pdb=" O ILE K 44 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE K 44 " --> pdb=" O HIS K 68 " (cutoff:3.500A) 182 hydrogen bonds defined for protein. 516 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: 0.53 Time building geometry restraints manager: 0.55 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: 1564 1.34 - 1.46: 679 1.46 - 1.57: 2795 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 5068 Sorted by residual: bond pdb=" N ASP B2027 " pdb=" CA ASP B2027 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.28e-02 6.10e+03 5.04e+00 bond pdb=" C ILE B2769 " pdb=" N SER B2770 " ideal model delta sigma weight residual 1.332 1.360 -0.027 1.40e-02 5.10e+03 3.83e+00 bond pdb=" N PHE B2796 " pdb=" CA PHE B2796 " ideal model delta sigma weight residual 1.467 1.487 -0.020 1.32e-02 5.74e+03 2.24e+00 bond pdb=" CA ILE B2769 " pdb=" CB ILE B2769 " ideal model delta sigma weight residual 1.540 1.559 -0.019 1.36e-02 5.41e+03 2.00e+00 bond pdb=" C GLN B2649 " pdb=" N PRO B2650 " ideal model delta sigma weight residual 1.335 1.353 -0.017 1.36e-02 5.41e+03 1.62e+00 ... (remaining 5063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 6625 2.28 - 4.56: 210 4.56 - 6.84: 27 6.84 - 9.12: 8 9.12 - 11.39: 2 Bond angle restraints: 6872 Sorted by residual: angle pdb=" CB ARG B2227 " pdb=" CG ARG B2227 " pdb=" CD ARG B2227 " ideal model delta sigma weight residual 111.30 122.69 -11.39 2.30e+00 1.89e-01 2.45e+01 angle pdb=" C ASP B2590 " pdb=" N ALA B2591 " pdb=" CA ALA B2591 " ideal model delta sigma weight residual 121.54 129.38 -7.84 1.91e+00 2.74e-01 1.68e+01 angle pdb=" CA ARG J 202 " pdb=" CB ARG J 202 " pdb=" CG ARG J 202 " ideal model delta sigma weight residual 114.10 121.76 -7.66 2.00e+00 2.50e-01 1.47e+01 angle pdb=" N PRO B2750 " pdb=" CA PRO B2750 " pdb=" C PRO B2750 " ideal model delta sigma weight residual 111.33 116.52 -5.19 1.43e+00 4.89e-01 1.32e+01 angle pdb=" N SER B2770 " pdb=" CA SER B2770 " pdb=" C SER B2770 " ideal model delta sigma weight residual 110.80 117.74 -6.94 2.13e+00 2.20e-01 1.06e+01 ... (remaining 6867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.40: 2935 28.40 - 56.80: 142 56.80 - 85.20: 12 85.20 - 113.60: 4 113.60 - 142.00: 3 Dihedral angle restraints: 3096 sinusoidal: 1231 harmonic: 1865 Sorted by residual: dihedral pdb=" CA MET B2643 " pdb=" C MET B2643 " pdb=" N LEU B2644 " pdb=" CA LEU B2644 " ideal model delta harmonic sigma weight residual 180.00 -155.26 -24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA SER B2770 " pdb=" C SER B2770 " pdb=" N ARG B2771 " pdb=" CA ARG B2771 " ideal model delta harmonic sigma weight residual -180.00 -156.89 -23.11 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" C1 SY8 K 101 " pdb=" C2 SY8 K 101 " pdb=" C3 SY8 K 101 " pdb=" C4 SY8 K 101 " ideal model delta sinusoidal sigma weight residual 57.79 -84.21 142.00 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 527 0.047 - 0.094: 188 0.094 - 0.140: 61 0.140 - 0.187: 9 0.187 - 0.234: 3 Chirality restraints: 788 Sorted by residual: chirality pdb=" CA ARG B2227 " pdb=" N ARG B2227 " pdb=" C ARG B2227 " pdb=" CB ARG B2227 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB ILE B2624 " pdb=" CA ILE B2624 " pdb=" CG1 ILE B2624 " pdb=" CG2 ILE B2624 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CG LEU B2606 " pdb=" CB LEU B2606 " pdb=" CD1 LEU B2606 " pdb=" CD2 LEU B2606 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.77e-01 ... (remaining 785 not shown) Planarity restraints: 903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B2774 " 0.073 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO B2775 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO B2775 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B2775 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B2507 " -0.059 5.00e-02 4.00e+02 9.00e-02 1.30e+01 pdb=" N PRO B2508 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO B2508 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B2508 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B2627 " 0.049 5.00e-02 4.00e+02 7.43e-02 8.82e+00 pdb=" N PRO B2628 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO B2628 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B2628 " 0.041 5.00e-02 4.00e+02 ... (remaining 900 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1353 2.81 - 3.33: 4229 3.33 - 3.86: 7701 3.86 - 4.38: 8457 4.38 - 4.90: 14631 Nonbonded interactions: 36371 Sorted by model distance: nonbonded pdb=" O ASN B2795 " pdb=" OD1 ASN B2795 " model vdw 2.288 3.040 nonbonded pdb=" O HIS B2761 " pdb=" OH TYR B2777 " model vdw 2.362 3.040 nonbonded pdb=" OG1 THR K 22 " pdb=" OD1 ASN K 25 " model vdw 2.362 3.040 nonbonded pdb=" O GLY B2683 " pdb=" OG SER B2738 " model vdw 2.383 3.040 nonbonded pdb=" O TYR B2731 " pdb=" NH2 ARG K 74 " model vdw 2.402 3.120 ... (remaining 36366 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 'I' and (resid 1 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 10 or (resid 11 and (name N or name CA \ or name C or name O or name CB )) or resid 12 through 28 or (resid 29 and (name \ N or name CA or name C or name O or name CB )) or resid 30 through 32 or (resid \ 33 and (name N or name CA or name C or name O or name CB )) or resid 34 through \ 43 or (resid 44 and (name N or name CA or name C or name O or name CB )) or res \ id 45 through 47 or resid 49 through 50 or (resid 51 through 52 and (name N or n \ ame CA or name C or name O or name CB )) or resid 53 or (resid 54 and (name N or \ name CA or name C or name O or name CB )) or resid 55 or (resid 56 and (name N \ or name CA or name C or name O or name CB )) or resid 57 through 72)) selection = (chain 'K' and (resid 1 through 47 or resid 49 through 72)) } 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: 13.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.280 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 5071 Z= 0.238 Angle : 0.941 11.394 6874 Z= 0.492 Chirality : 0.054 0.234 788 Planarity : 0.010 0.111 902 Dihedral : 16.627 142.004 1879 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.38 % Allowed : 0.94 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.00 (0.28), residues: 630 helix: -2.09 (0.26), residues: 256 sheet: -1.31 (0.85), residues: 43 loop : -1.97 (0.30), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B2227 TYR 0.013 0.002 TYR B2576 PHE 0.038 0.002 PHE B2218 TRP 0.011 0.002 TRP B2733 HIS 0.003 0.001 HIS B2020 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 5068) covalent geometry : angle 0.93873 ( 6872) hydrogen bonds : bond 0.17953 ( 182) hydrogen bonds : angle 7.75000 ( 516) Misc. bond : bond 0.06154 ( 2) link_TRANS : bond 0.00408 ( 1) link_TRANS : angle 3.66231 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.183 Fit side-chains REVERT: B 2666 SER cc_start: 0.7991 (p) cc_final: 0.7734 (p) REVERT: B 2743 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6945 (mm-30) outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 0.0903 time to fit residues: 11.9587 Evaluate side-chains 93 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2795 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 25 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: B2253 GLN B2564 ASN B2614 GLN J 192 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.128088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.110643 restraints weight = 11069.531| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.55 r_work: 0.3534 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 5071 Z= 0.246 Angle : 0.748 11.570 6874 Z= 0.389 Chirality : 0.048 0.166 788 Planarity : 0.008 0.078 902 Dihedral : 10.983 155.426 692 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 2.83 % Allowed : 13.40 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.31), residues: 630 helix: -0.96 (0.29), residues: 260 sheet: -1.70 (0.86), residues: 43 loop : -1.87 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B2248 TYR 0.013 0.002 TYR B2638 PHE 0.020 0.002 PHE B2710 TRP 0.021 0.003 TRP B2565 HIS 0.005 0.001 HIS B2566 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 5068) covalent geometry : angle 0.74846 ( 6872) hydrogen bonds : bond 0.05228 ( 182) hydrogen bonds : angle 5.68443 ( 516) Misc. bond : bond 0.00115 ( 2) link_TRANS : bond 0.00291 ( 1) link_TRANS : angle 0.67363 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.241 Fit side-chains REVERT: B 2666 SER cc_start: 0.8125 (p) cc_final: 0.7872 (p) REVERT: I 1 MET cc_start: 0.4592 (mmt) cc_final: 0.4349 (mmt) REVERT: K 27 LYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5753 (mtpp) outliers start: 15 outliers final: 11 residues processed: 104 average time/residue: 0.0799 time to fit residues: 10.7237 Evaluate side-chains 106 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2261 ASN Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2644 LEU Chi-restraints excluded: chain B residue 2716 SER Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain B residue 2795 ASN Chi-restraints excluded: chain K residue 27 LYS Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 7 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2564 ASN B2766 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.130663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.113315 restraints weight = 11114.583| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.54 r_work: 0.3585 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5071 Z= 0.122 Angle : 0.606 10.416 6874 Z= 0.315 Chirality : 0.043 0.146 788 Planarity : 0.006 0.060 902 Dihedral : 10.574 176.910 692 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.89 % Allowed : 17.74 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.32), residues: 630 helix: -0.34 (0.31), residues: 261 sheet: -2.04 (0.83), residues: 45 loop : -1.70 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B2248 TYR 0.014 0.001 TYR B2576 PHE 0.015 0.001 PHE B2710 TRP 0.007 0.001 TRP B2565 HIS 0.009 0.001 HIS B2275 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5068) covalent geometry : angle 0.60614 ( 6872) hydrogen bonds : bond 0.03827 ( 182) hydrogen bonds : angle 5.27304 ( 516) Misc. bond : bond 0.00089 ( 2) link_TRANS : bond 0.00247 ( 1) link_TRANS : angle 0.49334 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.220 Fit side-chains REVERT: B 2575 MET cc_start: 0.6536 (tpp) cc_final: 0.6219 (tpp) REVERT: B 2581 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.6841 (mp10) REVERT: B 2666 SER cc_start: 0.8046 (p) cc_final: 0.7813 (p) REVERT: K 27 LYS cc_start: 0.6151 (OUTLIER) cc_final: 0.5866 (mtpp) outliers start: 10 outliers final: 8 residues processed: 101 average time/residue: 0.0854 time to fit residues: 10.8446 Evaluate side-chains 106 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2257 ARG Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain K residue 27 LYS Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 30 optimal weight: 0.3980 chunk 2 optimal weight: 0.0470 chunk 52 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 0.2980 chunk 60 optimal weight: 0.0370 chunk 48 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.1756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2564 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.131337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.114055 restraints weight = 11006.031| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.55 r_work: 0.3593 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5071 Z= 0.111 Angle : 0.581 9.066 6874 Z= 0.302 Chirality : 0.042 0.144 788 Planarity : 0.006 0.054 902 Dihedral : 8.524 150.902 690 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 1.70 % Allowed : 19.81 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.32), residues: 630 helix: 0.06 (0.33), residues: 260 sheet: -2.14 (0.82), residues: 45 loop : -1.60 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B2227 TYR 0.013 0.001 TYR B2576 PHE 0.014 0.001 PHE B2218 TRP 0.003 0.001 TRP B2733 HIS 0.007 0.001 HIS B2275 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5068) covalent geometry : angle 0.58136 ( 6872) hydrogen bonds : bond 0.03340 ( 182) hydrogen bonds : angle 5.03662 ( 516) Misc. bond : bond 0.00081 ( 2) link_TRANS : bond 0.00244 ( 1) link_TRANS : angle 0.52279 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: B 2575 MET cc_start: 0.6591 (tpp) cc_final: 0.6383 (tpp) REVERT: B 2666 SER cc_start: 0.8112 (p) cc_final: 0.7868 (p) outliers start: 9 outliers final: 7 residues processed: 101 average time/residue: 0.0840 time to fit residues: 10.5941 Evaluate side-chains 102 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2716 SER Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 0.0770 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2564 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.128485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.110893 restraints weight = 11069.112| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.57 r_work: 0.3536 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 5071 Z= 0.186 Angle : 0.659 11.969 6874 Z= 0.341 Chirality : 0.045 0.162 788 Planarity : 0.006 0.052 902 Dihedral : 6.710 116.710 690 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.08 % Allowed : 21.32 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.32), residues: 630 helix: -0.03 (0.32), residues: 260 sheet: -2.70 (0.84), residues: 37 loop : -1.65 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B2227 TYR 0.014 0.002 TYR B2638 PHE 0.022 0.002 PHE B2218 TRP 0.014 0.002 TRP B2565 HIS 0.005 0.001 HIS B2275 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 5068) covalent geometry : angle 0.65930 ( 6872) hydrogen bonds : bond 0.04311 ( 182) hydrogen bonds : angle 5.13747 ( 516) Misc. bond : bond 0.00126 ( 2) link_TRANS : bond 0.00147 ( 1) link_TRANS : angle 0.48014 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.142 Fit side-chains REVERT: B 2581 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.6790 (mp10) REVERT: B 2666 SER cc_start: 0.8117 (p) cc_final: 0.7891 (p) outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 0.0786 time to fit residues: 10.0896 Evaluate side-chains 106 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2716 SER Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 59 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.0870 chunk 20 optimal weight: 0.0980 chunk 10 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 3 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 overall best weight: 0.1358 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.131010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.113664 restraints weight = 11229.884| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.58 r_work: 0.3586 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5071 Z= 0.108 Angle : 0.582 9.449 6874 Z= 0.301 Chirality : 0.042 0.144 788 Planarity : 0.006 0.053 902 Dihedral : 6.206 108.550 690 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 1.32 % Allowed : 23.02 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.33), residues: 630 helix: 0.25 (0.33), residues: 259 sheet: -2.66 (0.84), residues: 37 loop : -1.53 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2248 TYR 0.019 0.001 TYR B2576 PHE 0.017 0.001 PHE B2218 TRP 0.020 0.002 TRP B2565 HIS 0.008 0.001 HIS B2275 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 5068) covalent geometry : angle 0.58177 ( 6872) hydrogen bonds : bond 0.03218 ( 182) hydrogen bonds : angle 4.91802 ( 516) Misc. bond : bond 0.00065 ( 2) link_TRANS : bond 0.00011 ( 1) link_TRANS : angle 0.24941 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.209 Fit side-chains REVERT: B 2552 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7510 (mtp180) REVERT: B 2581 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.6787 (mp10) REVERT: B 2666 SER cc_start: 0.8051 (p) cc_final: 0.7837 (p) outliers start: 7 outliers final: 5 residues processed: 96 average time/residue: 0.0855 time to fit residues: 10.3972 Evaluate side-chains 100 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2552 ARG Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2716 SER Chi-restraints excluded: chain B residue 2759 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 42 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 13 optimal weight: 0.0570 chunk 7 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2564 ASN 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 = 0.130182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.112778 restraints weight = 11000.220| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.56 r_work: 0.3573 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5071 Z= 0.128 Angle : 0.597 9.368 6874 Z= 0.308 Chirality : 0.043 0.144 788 Planarity : 0.005 0.052 902 Dihedral : 5.966 99.794 690 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.64 % Allowed : 22.64 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.33), residues: 630 helix: 0.33 (0.33), residues: 259 sheet: -2.63 (0.84), residues: 37 loop : -1.48 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2227 TYR 0.013 0.001 TYR B2638 PHE 0.017 0.001 PHE B2218 TRP 0.011 0.001 TRP B2565 HIS 0.007 0.001 HIS B2275 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 5068) covalent geometry : angle 0.59672 ( 6872) hydrogen bonds : bond 0.03470 ( 182) hydrogen bonds : angle 4.90190 ( 516) Misc. bond : bond 0.00067 ( 2) link_TRANS : bond 0.00005 ( 1) link_TRANS : angle 0.27522 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.187 Fit side-chains REVERT: B 2552 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7535 (mtp180) REVERT: B 2581 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.6792 (mp10) REVERT: B 2666 SER cc_start: 0.8177 (p) cc_final: 0.7947 (p) outliers start: 14 outliers final: 9 residues processed: 100 average time/residue: 0.0789 time to fit residues: 9.9271 Evaluate side-chains 106 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2552 ARG Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2716 SER Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 60 optimal weight: 0.6980 chunk 14 optimal weight: 0.0670 chunk 20 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 33 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2564 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.131344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.114153 restraints weight = 11216.267| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.53 r_work: 0.3574 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5071 Z= 0.134 Angle : 0.619 9.549 6874 Z= 0.316 Chirality : 0.042 0.143 788 Planarity : 0.005 0.053 902 Dihedral : 5.819 94.477 690 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.45 % Allowed : 23.77 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.33), residues: 630 helix: 0.36 (0.33), residues: 259 sheet: -2.62 (0.84), residues: 37 loop : -1.47 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2227 TYR 0.022 0.002 TYR B2576 PHE 0.019 0.001 PHE B2218 TRP 0.009 0.001 TRP B2565 HIS 0.007 0.001 HIS B2275 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 5068) covalent geometry : angle 0.61871 ( 6872) hydrogen bonds : bond 0.03439 ( 182) hydrogen bonds : angle 4.90747 ( 516) Misc. bond : bond 0.00061 ( 2) link_TRANS : bond 0.00008 ( 1) link_TRANS : angle 0.25803 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: B 2552 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7511 (mtp180) outliers start: 13 outliers final: 11 residues processed: 102 average time/residue: 0.0799 time to fit residues: 10.3140 Evaluate side-chains 106 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2552 ARG Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2627 THR Chi-restraints excluded: chain B residue 2716 SER Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 40 optimal weight: 0.0570 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2564 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.128155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.110619 restraints weight = 11103.558| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.54 r_work: 0.3536 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 5071 Z= 0.212 Angle : 0.700 11.786 6874 Z= 0.360 Chirality : 0.045 0.160 788 Planarity : 0.006 0.053 902 Dihedral : 5.857 85.395 690 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 3.02 % Allowed : 24.53 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.46 (0.32), residues: 630 helix: 0.11 (0.32), residues: 260 sheet: -2.71 (0.82), residues: 37 loop : -1.67 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B2248 TYR 0.024 0.002 TYR B2576 PHE 0.021 0.002 PHE B2218 TRP 0.019 0.002 TRP B2565 HIS 0.006 0.002 HIS B2566 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 5068) covalent geometry : angle 0.69959 ( 6872) hydrogen bonds : bond 0.04282 ( 182) hydrogen bonds : angle 5.06885 ( 516) Misc. bond : bond 0.00094 ( 2) link_TRANS : bond 0.00059 ( 1) link_TRANS : angle 0.37393 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.248 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 104 average time/residue: 0.0817 time to fit residues: 10.8155 Evaluate side-chains 109 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2606 LEU Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2627 THR Chi-restraints excluded: chain B residue 2716 SER Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 9 optimal weight: 0.0670 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2564 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.129548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.112290 restraints weight = 11057.075| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.54 r_work: 0.3563 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5071 Z= 0.137 Angle : 0.650 11.053 6874 Z= 0.333 Chirality : 0.043 0.145 788 Planarity : 0.006 0.054 902 Dihedral : 5.615 78.600 690 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.64 % Allowed : 25.09 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.33), residues: 630 helix: 0.25 (0.33), residues: 260 sheet: -2.67 (0.81), residues: 37 loop : -1.61 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2227 TYR 0.023 0.002 TYR B2576 PHE 0.016 0.002 PHE B2710 TRP 0.009 0.001 TRP B2565 HIS 0.009 0.001 HIS B2275 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5068) covalent geometry : angle 0.65047 ( 6872) hydrogen bonds : bond 0.03620 ( 182) hydrogen bonds : angle 4.94878 ( 516) Misc. bond : bond 0.00054 ( 2) link_TRANS : bond 0.00006 ( 1) link_TRANS : angle 0.26911 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1260 Ramachandran restraints generated. 630 Oldfield, 0 Emsley, 630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.199 Fit side-chains REVERT: B 2581 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.6811 (mp10) REVERT: I 3 ILE cc_start: 0.7876 (mm) cc_final: 0.7609 (mm) REVERT: I 17 VAL cc_start: 0.6438 (m) cc_final: 0.6223 (m) outliers start: 14 outliers final: 10 residues processed: 103 average time/residue: 0.0870 time to fit residues: 11.3271 Evaluate side-chains 105 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2627 THR Chi-restraints excluded: chain B residue 2716 SER Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 42 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.0980 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2564 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.129001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.111553 restraints weight = 11287.304| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.58 r_work: 0.3556 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5071 Z= 0.159 Angle : 0.663 11.438 6874 Z= 0.339 Chirality : 0.044 0.150 788 Planarity : 0.006 0.054 902 Dihedral : 5.517 73.274 690 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.08 % Allowed : 25.85 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.33), residues: 630 helix: 0.22 (0.32), residues: 260 sheet: -2.69 (0.81), residues: 37 loop : -1.63 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2227 TYR 0.022 0.002 TYR B2576 PHE 0.017 0.002 PHE B2218 TRP 0.012 0.002 TRP B2565 HIS 0.009 0.001 HIS B2275 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 5068) covalent geometry : angle 0.66289 ( 6872) hydrogen bonds : bond 0.03780 ( 182) hydrogen bonds : angle 4.97086 ( 516) Misc. bond : bond 0.00064 ( 2) link_TRANS : bond 0.00043 ( 1) link_TRANS : angle 0.31925 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1383.91 seconds wall clock time: 24 minutes 28.41 seconds (1468.41 seconds total)