Starting phenix.real_space_refine on Tue Jan 14 02:12:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c07_16356/01_2025/8c07_16356.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c07_16356/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8c07_16356/01_2025/8c07_16356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c07_16356/01_2025/8c07_16356.map" model { file = "/net/cci-nas-00/data/ceres_data/8c07_16356/01_2025/8c07_16356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c07_16356/01_2025/8c07_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-5571/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: 6.18, per 1000 atoms: 1.24 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 655.2 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: 0.54 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: 1.30 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: 17.360 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 18.750 Find NCS groups from input model: 0.100 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:4.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.950 ------------------------------------------------------------------------------- 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 : 0.611 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: 0.1904 time to fit residues: 25.1305 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 : 0.574 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.127118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.109737 restraints weight = 11032.742| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.53 r_work: 0.3520 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 : 0.651 Fit side-chains REVERT: K 27 LYS cc_start: 0.6205 (OUTLIER) cc_final: 0.5751 (mtpp) outliers start: 17 outliers final: 12 residues processed: 103 average time/residue: 0.1900 time to fit residues: 24.8420 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 : 0.643 ------------------------------------------------------------------------------- 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 37 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 38 optimal weight: 0.0060 chunk 25 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 42 optimal weight: 0.4980 chunk 18 optimal weight: 0.1980 chunk 15 optimal weight: 0.0770 chunk 59 optimal weight: 0.0770 chunk 46 optimal weight: 0.9980 overall best weight: 0.1512 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.130980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.113800 restraints weight = 10956.581| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.51 r_work: 0.3590 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5068 Z= 0.161 Angle : 0.602 10.445 6872 Z= 0.312 Chirality : 0.043 0.145 788 Planarity : 0.006 0.061 902 Dihedral : 10.561 179.808 692 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.51 % Allowed : 18.87 % Favored : 79.62 % 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: -1.66 (0.32), residues: 630 helix: -0.26 (0.32), residues: 254 sheet: -2.03 (0.83), residues: 45 loop : -1.64 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B2565 HIS 0.008 0.001 HIS B2275 PHE 0.014 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 108 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: B 2060 ASN cc_start: 0.7346 (OUTLIER) cc_final: 0.6965 (t0) REVERT: B 2575 MET cc_start: 0.6540 (tpp) cc_final: 0.6239 (tpp) REVERT: B 2666 SER cc_start: 0.8105 (p) cc_final: 0.7865 (p) REVERT: K 27 LYS cc_start: 0.6233 (OUTLIER) cc_final: 0.5770 (mtpp) outliers start: 8 outliers final: 6 residues processed: 103 average time/residue: 0.1995 time to fit residues: 25.8886 Evaluate side-chains 106 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 31 optimal weight: 0.0170 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 0.0370 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.0010 chunk 12 optimal weight: 0.0470 chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 overall best weight: 0.0400 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.132547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.115138 restraints weight = 11231.286| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.61 r_work: 0.3610 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5068 Z= 0.155 Angle : 0.561 7.565 6872 Z= 0.291 Chirality : 0.041 0.142 788 Planarity : 0.006 0.054 902 Dihedral : 8.310 149.183 690 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.89 % Allowed : 19.81 % Favored : 78.30 % 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: -1.28 (0.33), residues: 630 helix: 0.13 (0.33), residues: 259 sheet: -1.95 (0.84), residues: 45 loop : -1.50 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B2565 HIS 0.007 0.001 HIS B2275 PHE 0.014 0.001 PHE B2218 TYR 0.013 0.001 TYR B2576 ARG 0.006 0.000 ARG B2248 *********************** 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: 10 poor density : 96 time to evaluate : 0.571 Fit side-chains REVERT: B 2060 ASN cc_start: 0.7330 (OUTLIER) cc_final: 0.6941 (t0) REVERT: B 2565 TRP cc_start: 0.8116 (OUTLIER) cc_final: 0.7566 (t-100) REVERT: B 2581 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.6798 (mp10) REVERT: B 2666 SER cc_start: 0.8138 (p) cc_final: 0.7890 (p) outliers start: 10 outliers final: 5 residues processed: 100 average time/residue: 0.1903 time to fit residues: 24.1520 Evaluate side-chains 102 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 2565 TRP 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 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 48 optimal weight: 0.0060 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 0.0060 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 overall best weight: 0.2812 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.130594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.113244 restraints weight = 11042.341| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.55 r_work: 0.3578 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1863 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 : 0.587 8.476 6872 Z= 0.304 Chirality : 0.042 0.143 788 Planarity : 0.006 0.052 902 Dihedral : 6.609 122.115 690 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.08 % Allowed : 20.75 % Favored : 77.17 % 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: -1.23 (0.33), residues: 630 helix: 0.22 (0.33), residues: 259 sheet: -2.54 (0.87), residues: 37 loop : -1.45 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B2565 HIS 0.005 0.001 HIS B2275 PHE 0.016 0.001 PHE B2218 TYR 0.013 0.001 TYR B2576 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 107 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: B 2666 SER cc_start: 0.8071 (p) cc_final: 0.7834 (p) outliers start: 11 outliers final: 8 residues processed: 100 average time/residue: 0.2109 time to fit residues: 27.0995 Evaluate side-chains 104 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 3 optimal weight: 0.0970 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.129383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.112017 restraints weight = 11128.710| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.55 r_work: 0.3561 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5068 Z= 0.225 Angle : 0.615 10.437 6872 Z= 0.317 Chirality : 0.043 0.153 788 Planarity : 0.006 0.051 902 Dihedral : 6.135 104.129 690 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.26 % Allowed : 21.70 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.26 (0.33), residues: 630 helix: 0.20 (0.33), residues: 260 sheet: -2.63 (0.85), residues: 37 loop : -1.47 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B2565 HIS 0.004 0.001 HIS B2275 PHE 0.021 0.002 PHE B2218 TYR 0.023 0.002 TYR B2576 ARG 0.005 0.000 ARG B2248 *********************** 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 108 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.658 Fit side-chains REVERT: B 2581 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.6781 (mp10) REVERT: B 2666 SER cc_start: 0.8149 (p) cc_final: 0.7928 (p) outliers start: 12 outliers final: 9 residues processed: 101 average time/residue: 0.2097 time to fit residues: 27.1557 Evaluate side-chains 105 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 66 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 0.0030 chunk 20 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.0970 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 overall best weight: 0.2788 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.130218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.112912 restraints weight = 10911.633| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.52 r_work: 0.3571 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2067 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= 0.197 Angle : 0.604 9.812 6872 Z= 0.311 Chirality : 0.043 0.144 788 Planarity : 0.005 0.051 902 Dihedral : 5.909 97.059 690 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.26 % Allowed : 22.83 % Favored : 74.91 % 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: -1.18 (0.33), residues: 630 helix: 0.31 (0.33), residues: 259 sheet: -2.61 (0.85), residues: 37 loop : -1.46 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B2565 HIS 0.009 0.001 HIS B2275 PHE 0.017 0.001 PHE B2218 TYR 0.019 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 106 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.627 Fit side-chains REVERT: B 2581 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.6735 (mp10) REVERT: B 2666 SER cc_start: 0.8157 (p) cc_final: 0.7932 (p) outliers start: 12 outliers final: 8 residues processed: 101 average time/residue: 0.1879 time to fit residues: 24.6999 Evaluate side-chains 104 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 51 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.0270 chunk 15 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.127535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.110004 restraints weight = 11221.764| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.55 r_work: 0.3522 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 5068 Z= 0.334 Angle : 0.719 13.100 6872 Z= 0.368 Chirality : 0.046 0.167 788 Planarity : 0.006 0.053 902 Dihedral : 5.964 83.008 690 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 2.64 % Allowed : 23.21 % Favored : 74.15 % 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: 260 sheet: -2.45 (0.91), residues: 32 loop : -1.73 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B2565 HIS 0.007 0.002 HIS B2275 PHE 0.026 0.002 PHE B2218 TYR 0.017 0.002 TYR B2576 ARG 0.004 0.001 ARG B2552 *********************** 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 108 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.685 Fit side-chains REVERT: B 2581 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.6834 (mp10) REVERT: B 2666 SER cc_start: 0.8172 (p) cc_final: 0.7961 (p) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.1714 time to fit residues: 22.6959 Evaluate side-chains 105 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 12 THR Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.321 > 50: distance: 77 - 82: 32.141 distance: 82 - 83: 11.662 distance: 83 - 84: 25.862 distance: 83 - 86: 34.389 distance: 84 - 85: 40.245 distance: 84 - 88: 14.064 distance: 86 - 87: 9.890 distance: 88 - 89: 41.971 distance: 89 - 90: 19.337 distance: 89 - 92: 42.222 distance: 90 - 91: 38.278 distance: 90 - 96: 61.875 distance: 92 - 93: 42.056 distance: 93 - 94: 10.901 distance: 93 - 95: 52.627 distance: 96 - 97: 41.858 distance: 96 - 102: 39.363 distance: 97 - 98: 45.178 distance: 97 - 100: 43.575 distance: 98 - 99: 22.793 distance: 98 - 103: 41.997 distance: 100 - 101: 27.859 distance: 101 - 102: 40.918 distance: 103 - 104: 51.750 distance: 104 - 105: 52.581 distance: 104 - 107: 4.876 distance: 105 - 106: 32.665 distance: 105 - 108: 17.483 distance: 108 - 109: 5.303 distance: 109 - 110: 41.697 distance: 109 - 112: 39.849 distance: 110 - 111: 47.251 distance: 110 - 114: 62.336 distance: 111 - 132: 26.777 distance: 112 - 113: 40.333 distance: 114 - 115: 10.451 distance: 115 - 116: 69.502 distance: 115 - 118: 45.348 distance: 116 - 117: 19.538 distance: 116 - 123: 40.490 distance: 118 - 119: 26.277 distance: 119 - 120: 20.479 distance: 120 - 121: 30.516 distance: 120 - 122: 36.747 distance: 123 - 124: 13.717 distance: 124 - 125: 47.083 distance: 124 - 127: 22.531 distance: 125 - 126: 20.901 distance: 125 - 132: 47.053 distance: 127 - 128: 30.035 distance: 128 - 129: 17.691 distance: 129 - 130: 17.928 distance: 129 - 131: 9.050 distance: 132 - 133: 14.464 distance: 133 - 134: 43.834 distance: 134 - 135: 31.068 distance: 134 - 136: 54.911 distance: 136 - 137: 44.259 distance: 137 - 138: 39.743 distance: 137 - 140: 13.061 distance: 138 - 139: 28.035 distance: 138 - 147: 46.627 distance: 140 - 141: 36.287 distance: 141 - 142: 36.880 distance: 141 - 143: 46.117 distance: 142 - 144: 33.761 distance: 143 - 145: 28.398 distance: 144 - 146: 15.974 distance: 145 - 146: 20.244 distance: 147 - 148: 40.540 distance: 148 - 149: 39.841 distance: 148 - 151: 70.530 distance: 149 - 150: 7.431 distance: 149 - 152: 34.062