Starting phenix.real_space_refine on Thu Mar 6 05:50:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c07_16356/03_2025/8c07_16356.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c07_16356/03_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_16356/03_2025/8c07_16356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c07_16356/03_2025/8c07_16356.map" model { file = "/net/cci-nas-00/data/ceres_data/8c07_16356/03_2025/8c07_16356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c07_16356/03_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-5624/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: 5.28, per 1000 atoms: 1.06 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: 1.47 Conformation dependent library (CDL) restraints added in 642.7 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: 0.62 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: 1.38 Time building geometry restraints manager: 1.58 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: 40.520 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.760 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:3.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.200 ------------------------------------------------------------------------------- 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 : 0.550 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: 0.2290 time to fit residues: 29.8654 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 : 0.598 ------------------------------------------------------------------------------- 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: 0.9990 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 = 43)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.109732 restraints weight = 11032.746| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.53 r_work: 0.3522 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1745 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 : 0.623 Fit side-chains REVERT: K 27 LYS cc_start: 0.6203 (OUTLIER) cc_final: 0.5746 (mtpp) outliers start: 17 outliers final: 12 residues processed: 103 average time/residue: 0.2143 time to fit residues: 28.3565 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 : 0.691 ------------------------------------------------------------------------------- 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: 0.5980 chunk 61 optimal weight: 0.7980 chunk 38 optimal weight: 0.0570 chunk 25 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.0170 chunk 59 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 overall best weight: 0.1536 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.131032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.113837 restraints weight = 10964.672| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.50 r_work: 0.3591 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1647 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= 0.159 Angle : 0.600 10.363 6872 Z= 0.311 Chirality : 0.043 0.146 788 Planarity : 0.006 0.061 902 Dihedral : 10.527 179.534 692 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.51 % Allowed : 19.06 % Favored : 79.43 % 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: -1.65 (0.32), residues: 630 helix: -0.25 (0.32), residues: 254 sheet: -2.03 (0.83), residues: 45 loop : -1.63 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B2565 HIS 0.009 0.001 HIS B2275 PHE 0.014 0.001 PHE B2710 TYR 0.016 0.001 TYR B2576 ARG 0.006 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 : 0.564 Fit side-chains REVERT: B 2060 ASN cc_start: 0.7320 (OUTLIER) cc_final: 0.6942 (t0) REVERT: B 2575 MET cc_start: 0.6531 (tpp) cc_final: 0.6232 (tpp) REVERT: B 2581 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.6805 (mp10) REVERT: B 2666 SER cc_start: 0.8087 (p) cc_final: 0.7848 (p) REVERT: K 27 LYS cc_start: 0.6237 (OUTLIER) cc_final: 0.5761 (mtpp) outliers start: 8 outliers final: 5 residues processed: 103 average time/residue: 0.2335 time to fit residues: 30.8801 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 : 0.487 ------------------------------------------------------------------------------- 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: 0.1980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 0.0020 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.129081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111395 restraints weight = 11131.462| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.58 r_work: 0.3544 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5068 Z= 0.251 Angle : 0.640 11.430 6872 Z= 0.331 Chirality : 0.044 0.157 788 Planarity : 0.006 0.053 902 Dihedral : 8.196 142.502 690 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.08 % Allowed : 20.94 % Favored : 76.98 % 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: -1.61 (0.32), residues: 630 helix: -0.11 (0.32), residues: 260 sheet: -2.32 (0.90), residues: 35 loop : -1.73 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B2565 HIS 0.007 0.001 HIS B2275 PHE 0.018 0.002 PHE B2710 TYR 0.014 0.001 TYR B2638 ARG 0.008 0.001 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 109 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.604 Fit side-chains REVERT: B 2575 MET cc_start: 0.6720 (tpp) cc_final: 0.6479 (tpp) REVERT: B 2581 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.6813 (mp10) REVERT: B 2666 SER cc_start: 0.8111 (p) cc_final: 0.7887 (p) REVERT: K 27 LYS cc_start: 0.6189 (OUTLIER) cc_final: 0.5713 (mtpp) outliers start: 11 outliers final: 9 residues processed: 101 average time/residue: 0.1790 time to fit residues: 22.9203 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 : 0.621 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.0060 chunk 59 optimal weight: 0.0870 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 overall best weight: 0.3374 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.129516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.111896 restraints weight = 11077.056| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.57 r_work: 0.3554 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5068 Z= 0.218 Angle : 0.617 11.058 6872 Z= 0.320 Chirality : 0.043 0.152 788 Planarity : 0.006 0.052 902 Dihedral : 6.787 120.329 690 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.02 % Allowed : 21.32 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.48 (0.32), residues: 630 helix: 0.11 (0.32), residues: 253 sheet: -2.61 (0.85), residues: 37 loop : -1.67 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B2565 HIS 0.007 0.001 HIS B2275 PHE 0.017 0.002 PHE B2710 TYR 0.020 0.002 TYR B2576 ARG 0.004 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 115 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.879 Fit side-chains REVERT: B 2552 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7716 (mtm180) REVERT: B 2581 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.6794 (mp10) REVERT: B 2666 SER cc_start: 0.8063 (p) cc_final: 0.7818 (p) REVERT: B 2667 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8601 (mt) REVERT: K 27 LYS cc_start: 0.6183 (OUTLIER) cc_final: 0.5708 (mtpp) outliers start: 16 outliers final: 10 residues processed: 106 average time/residue: 0.2399 time to fit residues: 33.1668 Evaluate side-chains 111 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2552 ARG Chi-restraints excluded: chain B residue 2564 ASN Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2584 LEU Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2667 LEU Chi-restraints excluded: chain B residue 2716 SER Chi-restraints excluded: chain B residue 2759 ASP Chi-restraints excluded: chain B residue 2787 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.3980 chunk 7 optimal weight: 0.0970 chunk 30 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 59 optimal weight: 0.0570 chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.0980 chunk 3 optimal weight: 0.0870 overall best weight: 0.0852 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.131716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.114381 restraints weight = 11060.754| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.57 r_work: 0.3598 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2030 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= 0.152 Angle : 0.572 8.597 6872 Z= 0.296 Chirality : 0.041 0.142 788 Planarity : 0.006 0.053 902 Dihedral : 6.187 109.941 690 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.26 % Allowed : 23.21 % 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: -1.24 (0.33), residues: 630 helix: 0.32 (0.33), residues: 259 sheet: -2.51 (0.87), residues: 37 loop : -1.56 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B2713 HIS 0.007 0.001 HIS B2275 PHE 0.018 0.001 PHE B2218 TYR 0.017 0.001 TYR B2576 ARG 0.003 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 107 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.533 Fit side-chains REVERT: B 2552 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7578 (mtm180) REVERT: B 2581 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.6797 (mp10) REVERT: B 2666 SER cc_start: 0.8063 (p) cc_final: 0.7835 (p) outliers start: 12 outliers final: 6 residues processed: 101 average time/residue: 0.1967 time to fit residues: 25.2241 Evaluate side-chains 103 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2019 ASN Chi-restraints excluded: chain B residue 2301 GLN Chi-restraints excluded: chain B residue 2552 ARG Chi-restraints excluded: chain B residue 2581 GLN Chi-restraints excluded: chain B residue 2624 ILE Chi-restraints excluded: chain B residue 2716 SER Chi-restraints excluded: chain B residue 2759 ASP 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: 0.1980 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 20 optimal weight: 0.0870 chunk 46 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.130095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.112641 restraints weight = 10929.373| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.53 r_work: 0.3563 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2096 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= 0.215 Angle : 0.608 9.426 6872 Z= 0.313 Chirality : 0.043 0.145 788 Planarity : 0.006 0.056 902 Dihedral : 6.034 102.203 690 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.21 % Allowed : 22.83 % Favored : 73.96 % 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: -1.22 (0.33), residues: 630 helix: 0.33 (0.33), residues: 259 sheet: -2.58 (0.85), residues: 37 loop : -1.54 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B2565 HIS 0.005 0.001 HIS B2275 PHE 0.018 0.002 PHE B2218 TYR 0.013 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: 17 poor density : 92 time to evaluate : 0.591 Fit side-chains REVERT: B 2581 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.6751 (mp10) REVERT: B 2666 SER cc_start: 0.8122 (p) cc_final: 0.7899 (p) outliers start: 17 outliers final: 13 residues processed: 100 average time/residue: 0.3195 time to fit residues: 41.3798 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 : 0.708 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 40 optimal weight: 0.0040 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.0170 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 chunk 36 optimal weight: 0.0570 chunk 61 optimal weight: 0.7980 overall best weight: 0.1666 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.130862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.113556 restraints weight = 11188.803| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.57 r_work: 0.3588 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5068 Z= 0.174 Angle : 0.595 9.366 6872 Z= 0.305 Chirality : 0.042 0.147 788 Planarity : 0.005 0.056 902 Dihedral : 5.784 95.902 690 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.26 % Allowed : 24.34 % Favored : 73.40 % 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: 259 sheet: -2.50 (0.85), residues: 37 loop : -1.45 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B2565 HIS 0.006 0.001 HIS B2275 PHE 0.013 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 108 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.139 Fit side-chains REVERT: B 2581 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.6815 (mp10) REVERT: B 2666 SER cc_start: 0.8073 (p) cc_final: 0.7853 (p) outliers start: 12 outliers final: 8 residues processed: 102 average time/residue: 0.2752 time to fit residues: 36.2372 Evaluate side-chains 102 residues out of total 575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 2716 SER Chi-restraints excluded: chain B residue 2742 SER Chi-restraints excluded: chain B residue 2759 ASP 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-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 64.2032 > 50: distance: 77 - 82: 15.824 distance: 82 - 83: 19.570 distance: 83 - 84: 13.802 distance: 83 - 86: 23.785 distance: 84 - 85: 41.722 distance: 84 - 88: 15.743 distance: 86 - 87: 28.220 distance: 88 - 89: 40.221 distance: 89 - 90: 4.806 distance: 89 - 92: 31.459 distance: 90 - 91: 34.517 distance: 90 - 96: 13.596 distance: 92 - 93: 21.333 distance: 93 - 94: 8.475 distance: 93 - 95: 22.325 distance: 96 - 97: 26.662 distance: 96 - 102: 29.882 distance: 97 - 98: 34.440 distance: 97 - 100: 42.393 distance: 98 - 99: 15.887 distance: 98 - 103: 30.304 distance: 100 - 101: 43.164 distance: 101 - 102: 10.401 distance: 103 - 104: 24.991 distance: 104 - 105: 7.349 distance: 104 - 107: 34.565 distance: 105 - 106: 19.627 distance: 108 - 109: 33.548 distance: 109 - 110: 26.867 distance: 109 - 112: 34.355 distance: 110 - 111: 21.417 distance: 110 - 114: 22.409 distance: 111 - 132: 35.257 distance: 112 - 113: 13.436 distance: 114 - 115: 10.544 distance: 115 - 116: 16.470 distance: 115 - 118: 14.276 distance: 116 - 117: 26.307 distance: 116 - 123: 19.797 distance: 118 - 119: 14.463 distance: 119 - 120: 21.578 distance: 120 - 121: 25.137 distance: 120 - 122: 31.515 distance: 123 - 124: 16.238 distance: 124 - 125: 5.047 distance: 124 - 127: 7.076 distance: 125 - 126: 14.556 distance: 125 - 132: 15.452 distance: 127 - 128: 15.897 distance: 129 - 130: 5.911 distance: 129 - 131: 5.305 distance: 132 - 133: 28.475 distance: 133 - 134: 26.815 distance: 134 - 135: 24.879 distance: 134 - 136: 34.574 distance: 136 - 137: 19.392 distance: 137 - 138: 39.752 distance: 137 - 140: 18.404 distance: 138 - 139: 15.359 distance: 138 - 147: 9.138 distance: 140 - 141: 21.351 distance: 141 - 142: 23.079 distance: 141 - 143: 10.246 distance: 142 - 144: 16.770 distance: 143 - 145: 6.983 distance: 144 - 146: 6.472 distance: 145 - 146: 11.610 distance: 147 - 148: 7.950 distance: 148 - 149: 12.043 distance: 148 - 151: 17.826 distance: 149 - 150: 26.852 distance: 149 - 152: 20.709