Starting phenix.real_space_refine on Fri Dec 27 13:35:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c07_16356/12_2024/8c07_16356.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c07_16356/12_2024/8c07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8c07_16356/12_2024/8c07_16356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c07_16356/12_2024/8c07_16356.map" model { file = "/net/cci-nas-00/data/ceres_data/8c07_16356/12_2024/8c07_16356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c07_16356/12_2024/8c07_16356.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 10, 'ARG: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, 'ARG:plan': 1, 'ASP: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: 6.22, per 1000 atoms: 1.25 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: 1.26 Conformation dependent library (CDL) restraints added in 634.5 milliseconds 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: 0.60 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: 1.29 Time building geometry restraints manager: 1.41 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: 10.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.630 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.300 ------------------------------------------------------------------------------- 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 0.045 5068 Z= 0.268 Angle : 0.939 11.394 6872 Z= 0.491 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.002 TRP B2733 HIS 0.003 0.001 HIS B2020 PHE 0.038 0.002 PHE B2218 TYR 0.013 0.002 TYR B2576 ARG 0.014 0.001 ARG B2227 *********************** 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 : 0.558 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: 0.2030 time to fit residues: 26.7518 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 : 0.619 ------------------------------------------------------------------------------- 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 53 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2060 ASN B2253 GLN B2564 ASN B2614 GLN J 192 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 5068 Z= 0.419 Angle : 0.798 13.123 6872 Z= 0.414 Chirality : 0.050 0.173 788 Planarity : 0.008 0.080 902 Dihedral : 11.073 158.136 692 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 3.21 % Allowed : 13.21 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.30), residues: 630 helix: -1.04 (0.29), residues: 260 sheet: -1.84 (0.84), residues: 43 loop : -1.93 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B2565 HIS 0.006 0.002 HIS B2566 PHE 0.021 0.003 PHE B2710 TYR 0.015 0.002 TYR B2638 ARG 0.006 0.001 ARG B2248 *********************** 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 115 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.631 Fit side-chains REVERT: K 27 LYS cc_start: 0.6230 (OUTLIER) cc_final: 0.5852 (mtpp) outliers start: 17 outliers final: 12 residues processed: 103 average time/residue: 0.2342 time to fit residues: 31.2299 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 : 0.622 ------------------------------------------------------------------------------- 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 12 THR 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 31 optimal weight: 0.0000 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 15 optimal weight: 0.0980 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 19 optimal weight: 0.0370 chunk 45 optimal weight: 0.0970 overall best weight: 0.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5068 Z= 0.154 Angle : 0.592 9.772 6872 Z= 0.306 Chirality : 0.042 0.145 788 Planarity : 0.006 0.062 902 Dihedral : 10.488 179.566 692 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.51 % Allowed : 18.30 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.32), residues: 630 helix: -0.20 (0.32), residues: 253 sheet: -1.99 (0.84), residues: 45 loop : -1.60 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B2565 HIS 0.009 0.001 HIS B2275 PHE 0.013 0.001 PHE B2710 TYR 0.016 0.001 TYR B2576 ARG 0.005 0.000 ARG B2248 *********************** 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 107 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.801 Fit side-chains REVERT: B 2060 ASN cc_start: 0.6929 (OUTLIER) cc_final: 0.6595 (t0) REVERT: B 2575 MET cc_start: 0.6085 (tpp) cc_final: 0.5795 (tpp) REVERT: B 2581 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.6567 (mp10) REVERT: B 2666 SER cc_start: 0.8044 (p) cc_final: 0.7794 (p) REVERT: K 27 LYS cc_start: 0.6218 (OUTLIER) cc_final: 0.5801 (mtpp) outliers start: 8 outliers final: 5 residues processed: 102 average time/residue: 0.2364 time to fit residues: 31.2068 Evaluate side-chains 105 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2060 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 2624 ILE Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain K residue 27 LYS 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 43 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 54 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 : 0.004 0.045 5068 Z= 0.240 Angle : 0.623 10.751 6872 Z= 0.324 Chirality : 0.044 0.157 788 Planarity : 0.006 0.053 902 Dihedral : 8.407 146.782 690 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 1.89 % Allowed : 20.38 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.32), residues: 630 helix: -0.07 (0.32), residues: 260 sheet: -2.56 (0.87), residues: 37 loop : -1.66 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B2565 HIS 0.007 0.001 HIS B2275 PHE 0.017 0.002 PHE B2710 TYR 0.014 0.001 TYR B2638 ARG 0.004 0.000 ARG B2227 *********************** 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 110 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.620 Fit side-chains REVERT: B 2575 MET cc_start: 0.6297 (tpp) cc_final: 0.6012 (tpp) REVERT: B 2581 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.6509 (mp10) REVERT: B 2666 SER cc_start: 0.8131 (p) cc_final: 0.7893 (p) REVERT: K 27 LYS cc_start: 0.6213 (OUTLIER) cc_final: 0.5818 (mtpp) outliers start: 10 outliers final: 8 residues processed: 103 average time/residue: 0.1907 time to fit residues: 24.9028 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 : 0.623 ------------------------------------------------------------------------------- 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 27 LYS 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 50 optimal weight: 0.9990 chunk 34 optimal weight: 0.0870 chunk 0 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.0980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5068 Z= 0.256 Angle : 0.640 11.573 6872 Z= 0.332 Chirality : 0.044 0.157 788 Planarity : 0.006 0.053 902 Dihedral : 6.927 122.279 690 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.64 % Allowed : 20.94 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.32), residues: 630 helix: 0.01 (0.32), residues: 254 sheet: -2.65 (0.85), residues: 37 loop : -1.68 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B2565 HIS 0.007 0.001 HIS B2275 PHE 0.019 0.002 PHE B2710 TYR 0.013 0.001 TYR B2638 ARG 0.005 0.000 ARG B2227 *********************** 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 110 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.612 Fit side-chains REVERT: B 2575 MET cc_start: 0.6353 (tpp) cc_final: 0.6143 (tpp) REVERT: B 2581 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.6517 (mp10) REVERT: B 2666 SER cc_start: 0.8133 (p) cc_final: 0.7901 (p) REVERT: K 27 LYS cc_start: 0.6214 (OUTLIER) cc_final: 0.5811 (mtpp) outliers start: 14 outliers final: 9 residues processed: 101 average time/residue: 0.1916 time to fit residues: 24.7194 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 : 0.610 ------------------------------------------------------------------------------- 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 12 THR Chi-restraints excluded: chain K residue 27 LYS 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 54 optimal weight: 0.9990 chunk 12 optimal weight: 0.0170 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 58 optimal weight: 0.2980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5068 Z= 0.199 Angle : 0.604 10.860 6872 Z= 0.313 Chirality : 0.043 0.149 788 Planarity : 0.006 0.052 902 Dihedral : 6.386 110.808 690 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.02 % Allowed : 22.45 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.32), residues: 630 helix: 0.13 (0.33), residues: 259 sheet: -2.66 (0.84), residues: 37 loop : -1.65 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B2565 HIS 0.006 0.001 HIS B2275 PHE 0.016 0.001 PHE B2710 TYR 0.024 0.002 TYR B2576 ARG 0.003 0.000 ARG B2552 *********************** 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 111 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.961 Fit side-chains REVERT: B 2581 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.6484 (mp10) REVERT: B 2666 SER cc_start: 0.8100 (p) cc_final: 0.7854 (p) REVERT: B 2667 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8671 (mt) REVERT: K 27 LYS cc_start: 0.6162 (OUTLIER) cc_final: 0.5768 (mtpp) outliers start: 16 outliers final: 10 residues processed: 103 average time/residue: 0.2246 time to fit residues: 29.5592 Evaluate side-chains 105 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 2584 LEU Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2627 THR Chi-restraints excluded: chain B residue 2667 LEU 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 12 THR Chi-restraints excluded: chain K residue 27 LYS Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.1980 chunk 34 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 0.0970 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 18 optimal weight: 0.0980 overall best weight: 0.2378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5068 Z= 0.186 Angle : 0.601 9.896 6872 Z= 0.309 Chirality : 0.042 0.143 788 Planarity : 0.006 0.053 902 Dihedral : 6.066 102.066 690 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.83 % Allowed : 23.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.33), residues: 630 helix: 0.26 (0.33), residues: 259 sheet: -2.65 (0.83), residues: 37 loop : -1.57 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2565 HIS 0.007 0.001 HIS B2275 PHE 0.017 0.001 PHE B2218 TYR 0.020 0.001 TYR B2576 ARG 0.003 0.000 ARG B2248 *********************** 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 109 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.623 Fit side-chains REVERT: B 2581 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.6461 (mp10) REVERT: B 2666 SER cc_start: 0.8088 (p) cc_final: 0.7841 (p) REVERT: K 27 LYS cc_start: 0.6171 (OUTLIER) cc_final: 0.5765 (mtpp) outliers start: 15 outliers final: 10 residues processed: 101 average time/residue: 0.1973 time to fit residues: 25.0016 Evaluate side-chains 109 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 2624 ILE Chi-restraints excluded: chain B residue 2716 SER Chi-restraints excluded: chain B residue 2742 SER Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 27 LYS 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 11 optimal weight: 0.0370 chunk 38 optimal weight: 0.0980 chunk 41 optimal weight: 0.0870 chunk 30 optimal weight: 0.0980 chunk 5 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 0.0970 chunk 53 optimal weight: 0.0060 chunk 56 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 overall best weight: 0.0650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5068 Z= 0.147 Angle : 0.576 9.468 6872 Z= 0.293 Chirality : 0.042 0.153 788 Planarity : 0.005 0.054 902 Dihedral : 5.739 95.643 690 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.26 % Allowed : 24.15 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.34), residues: 630 helix: 0.46 (0.34), residues: 259 sheet: -2.49 (0.85), residues: 37 loop : -1.43 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B2713 HIS 0.007 0.001 HIS B2275 PHE 0.011 0.001 PHE B2218 TYR 0.021 0.001 TYR B2576 ARG 0.003 0.000 ARG B2227 *********************** 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 112 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.634 Fit side-chains REVERT: B 2581 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.6507 (mp10) REVERT: B 2666 SER cc_start: 0.8029 (p) cc_final: 0.7822 (p) outliers start: 12 outliers final: 8 residues processed: 106 average time/residue: 0.1970 time to fit residues: 26.6275 Evaluate side-chains 105 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2304 LEU 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 2742 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.0870 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.0170 chunk 36 optimal weight: 0.3980 chunk 28 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 overall best weight: 0.2596 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5068 Z= 0.198 Angle : 0.612 10.607 6872 Z= 0.311 Chirality : 0.042 0.144 788 Planarity : 0.005 0.051 902 Dihedral : 5.524 85.659 690 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.26 % Allowed : 25.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.34), residues: 630 helix: 0.42 (0.33), residues: 260 sheet: -2.59 (0.84), residues: 37 loop : -1.45 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B2565 HIS 0.005 0.001 HIS B2275 PHE 0.018 0.001 PHE B2218 TYR 0.021 0.001 TYR B2576 ARG 0.006 0.000 ARG B2248 *********************** 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 109 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.555 Fit side-chains REVERT: B 2581 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.6504 (mp10) REVERT: B 2609 GLU cc_start: 0.7493 (mp0) cc_final: 0.7274 (mp0) REVERT: B 2666 SER cc_start: 0.8046 (p) cc_final: 0.7807 (p) outliers start: 12 outliers final: 10 residues processed: 103 average time/residue: 0.1926 time to fit residues: 25.3376 Evaluate side-chains 109 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2304 LEU 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 2742 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 0.0570 chunk 38 optimal weight: 0.3980 chunk 30 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 53 optimal weight: 0.0170 chunk 15 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 7 optimal weight: 0.0980 overall best weight: 0.1536 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 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 0.170 5068 Z= 0.233 Angle : 1.094 59.193 6872 Z= 0.644 Chirality : 0.046 0.491 788 Planarity : 0.006 0.052 902 Dihedral : 5.583 85.536 690 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.26 % Allowed : 25.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.34), residues: 630 helix: 0.43 (0.33), residues: 260 sheet: -2.59 (0.84), residues: 37 loop : -1.44 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B2565 HIS 0.005 0.001 HIS B2275 PHE 0.016 0.001 PHE B2218 TYR 0.019 0.001 TYR B2576 ARG 0.012 0.000 ARG B2248 ********************** 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 108 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.598 Fit side-chains REVERT: B 2581 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.6505 (mp10) REVERT: B 2666 SER cc_start: 0.8041 (p) cc_final: 0.7801 (p) outliers start: 12 outliers final: 11 residues processed: 104 average time/residue: 0.1840 time to fit residues: 24.3731 Evaluate side-chains 109 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2304 LEU 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 2742 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.0770 chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B2564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.130753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.113409 restraints weight = 10968.972| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.52 r_work: 0.3585 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.169 5068 Z= 0.309 Angle : 0.812 23.238 6872 Z= 0.497 Chirality : 0.044 0.311 788 Planarity : 0.007 0.097 902 Dihedral : 5.583 85.536 690 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.26 % Allowed : 25.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.34), residues: 630 helix: 0.43 (0.33), residues: 260 sheet: -2.59 (0.84), residues: 37 loop : -1.44 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B2565 HIS 0.005 0.001 HIS B2275 PHE 0.016 0.001 PHE B2218 TYR 0.019 0.001 TYR B2576 ARG 0.012 0.000 ARG B2248 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1984.10 seconds wall clock time: 39 minutes 35.36 seconds (2375.36 seconds total)