Starting phenix.real_space_refine on Fri Aug 22 21:05:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8emr_28262/08_2025/8emr_28262.cif Found real_map, /net/cci-nas-00/data/ceres_data/8emr_28262/08_2025/8emr_28262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8emr_28262/08_2025/8emr_28262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8emr_28262/08_2025/8emr_28262.map" model { file = "/net/cci-nas-00/data/ceres_data/8emr_28262/08_2025/8emr_28262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8emr_28262/08_2025/8emr_28262.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.030 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 35 5.16 5 C 4880 2.51 5 N 1329 2.21 5 O 1439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7685 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 859, 6930 Classifications: {'peptide': 859} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 56, 'TRANS': 798} Chain breaks: 2 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 703 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.77, per 1000 atoms: 0.23 Number of scatterers: 7685 At special positions: 0 Unit cell: (70.2, 87.48, 122.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 35 16.00 O 1439 8.00 N 1329 7.00 C 4880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 644 " distance=2.03 Simple disulfide: pdb=" SG CYS B 77 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 116 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG D 1 " - " ASN A 97 " Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 372.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1758 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 22.0% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 34 through 38 removed outlier: 3.530A pdb=" N ASN A 37 " --> pdb=" O ASP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 371 through 384 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.873A pdb=" N VAL A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.662A pdb=" N LYS A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 removed outlier: 3.900A pdb=" N GLU A 481 " --> pdb=" O TYR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.674A pdb=" N ARG A 610 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 638 removed outlier: 4.580A pdb=" N ILE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 656 through 668 Processing helix chain 'A' and resid 690 through 707 removed outlier: 3.661A pdb=" N ASP A 695 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 722 Processing helix chain 'A' and resid 728 through 733 removed outlier: 4.434A pdb=" N GLN A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.804A pdb=" N ASN A 741 " --> pdb=" O THR A 738 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 742 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 852 through 857 removed outlier: 3.572A pdb=" N THR A 856 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 69 removed outlier: 10.464A pdb=" N LEU A 64 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 11.898A pdb=" N ILE A 79 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 66 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A 77 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY A 93 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 69 removed outlier: 10.464A pdb=" N LEU A 64 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 11.898A pdb=" N ILE A 79 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 66 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A 77 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS A 255 " --> pdb=" O HIS A 305 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.559A pdb=" N SER A 129 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU A 139 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ARG A 133 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.559A pdb=" N SER A 129 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU A 139 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ARG A 133 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 157 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 158 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 160 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA6, first strand: chain 'A' and resid 537 through 540 removed outlier: 7.299A pdb=" N HIS A 397 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 726 through 727 removed outlier: 3.876A pdb=" N LEU A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 764 through 769 Processing sheet with id=AA9, first strand: chain 'A' and resid 808 through 812 removed outlier: 6.081A pdb=" N ILE A 828 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 891 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N TRP A 888 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY A 932 " --> pdb=" O TRP A 888 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU A 890 " --> pdb=" O LYS A 930 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 839 through 846 Processing sheet with id=AB2, first strand: chain 'B' and resid 74 through 76 277 hydrogen bonds defined for protein. 732 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: 1.05 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1278 1.32 - 1.44: 2277 1.44 - 1.57: 4299 1.57 - 1.69: 0 1.69 - 1.82: 53 Bond restraints: 7907 Sorted by residual: bond pdb=" CA ARG A 818 " pdb=" C ARG A 818 " ideal model delta sigma weight residual 1.523 1.441 0.082 1.30e-02 5.92e+03 4.02e+01 bond pdb=" C ARG A 817 " pdb=" N ARG A 818 " ideal model delta sigma weight residual 1.335 1.405 -0.070 1.31e-02 5.83e+03 2.83e+01 bond pdb=" CA SER A 819 " pdb=" C SER A 819 " ideal model delta sigma weight residual 1.525 1.459 0.066 1.25e-02 6.40e+03 2.82e+01 bond pdb=" C SER A 819 " pdb=" O SER A 819 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.08e-02 8.57e+03 1.64e+01 bond pdb=" C ARG A 818 " pdb=" O ARG A 818 " ideal model delta sigma weight residual 1.237 1.191 0.045 1.17e-02 7.31e+03 1.51e+01 ... (remaining 7902 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 10423 1.44 - 2.89: 252 2.89 - 4.33: 58 4.33 - 5.78: 29 5.78 - 7.22: 6 Bond angle restraints: 10768 Sorted by residual: angle pdb=" N GLY A 612 " pdb=" CA GLY A 612 " pdb=" C GLY A 612 " ideal model delta sigma weight residual 110.20 115.31 -5.11 1.32e+00 5.74e-01 1.50e+01 angle pdb=" N ARG A 817 " pdb=" CA ARG A 817 " pdb=" C ARG A 817 " ideal model delta sigma weight residual 109.41 103.74 5.67 1.52e+00 4.33e-01 1.39e+01 angle pdb=" C ARG A 817 " pdb=" N ARG A 818 " pdb=" CA ARG A 818 " ideal model delta sigma weight residual 120.28 125.13 -4.85 1.34e+00 5.57e-01 1.31e+01 angle pdb=" C MET A 814 " pdb=" N ARG A 815 " pdb=" CA ARG A 815 " ideal model delta sigma weight residual 123.05 118.19 4.86 1.40e+00 5.10e-01 1.20e+01 angle pdb=" CA ARG A 817 " pdb=" C ARG A 817 " pdb=" N ARG A 818 " ideal model delta sigma weight residual 115.42 121.07 -5.65 1.64e+00 3.72e-01 1.19e+01 ... (remaining 10763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 4394 21.81 - 43.62: 277 43.62 - 65.43: 24 65.43 - 87.24: 14 87.24 - 109.05: 9 Dihedral angle restraints: 4718 sinusoidal: 1972 harmonic: 2746 Sorted by residual: dihedral pdb=" CB CYS B 100 " pdb=" SG CYS B 100 " pdb=" SG CYS B 116 " pdb=" CB CYS B 116 " ideal model delta sinusoidal sigma weight residual -86.00 -156.29 70.29 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS B 77 " pdb=" SG CYS B 77 " pdb=" SG CYS B 99 " pdb=" CB CYS B 99 " ideal model delta sinusoidal sigma weight residual 93.00 60.24 32.76 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" C MET A 814 " pdb=" N MET A 814 " pdb=" CA MET A 814 " pdb=" CB MET A 814 " ideal model delta harmonic sigma weight residual -122.60 -132.11 9.51 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 4715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1066 0.090 - 0.181: 75 0.181 - 0.271: 0 0.271 - 0.362: 1 0.362 - 0.452: 1 Chirality restraints: 1143 Sorted by residual: chirality pdb=" CA MET A 814 " pdb=" N MET A 814 " pdb=" C MET A 814 " pdb=" CB MET A 814 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA TRP A 503 " pdb=" N TRP A 503 " pdb=" C TRP A 503 " pdb=" CB TRP A 503 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 1140 not shown) Planarity restraints: 1413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 489 " 0.020 2.00e-02 2.50e+03 1.70e-02 5.75e+00 pdb=" CG TYR A 489 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 489 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 489 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 489 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 489 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 489 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 489 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 87 " 0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO B 88 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 306 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 307 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " 0.023 5.00e-02 4.00e+02 ... (remaining 1410 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1713 2.79 - 3.32: 6617 3.32 - 3.84: 12673 3.84 - 4.37: 15067 4.37 - 4.90: 26466 Nonbonded interactions: 62536 Sorted by model distance: nonbonded pdb=" OH TYR A 257 " pdb=" O PHE A 740 " model vdw 2.263 3.040 nonbonded pdb=" O ARG B 91 " pdb="CA CA B 601 " model vdw 2.275 2.510 nonbonded pdb=" OD2 ASP A 848 " pdb=" OG1 THR A 851 " model vdw 2.284 3.040 nonbonded pdb=" O VAL B 96 " pdb="CA CA B 601 " model vdw 2.303 2.510 nonbonded pdb=" OD2 ASP B 104 " pdb="CA CA B 601 " model vdw 2.316 2.510 ... (remaining 62531 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.020 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.270 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 : 0.003 0.082 7915 Z= 0.211 Angle : 0.628 7.221 10788 Z= 0.332 Chirality : 0.046 0.452 1143 Planarity : 0.005 0.046 1412 Dihedral : 14.915 109.049 2948 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.12 % Allowed : 0.24 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.27), residues: 944 helix: 1.26 (0.42), residues: 153 sheet: 0.46 (0.36), residues: 241 loop : -1.32 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 817 TYR 0.042 0.001 TYR A 489 PHE 0.014 0.001 PHE A 673 TRP 0.017 0.001 TRP A 503 HIS 0.004 0.001 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7907) covalent geometry : angle 0.62433 (10768) SS BOND : bond 0.00176 ( 4) SS BOND : angle 0.54094 ( 8) hydrogen bonds : bond 0.16260 ( 253) hydrogen bonds : angle 6.21787 ( 732) link_ALPHA1-3 : bond 0.00509 ( 1) link_ALPHA1-3 : angle 1.62715 ( 3) link_BETA1-4 : bond 0.00959 ( 2) link_BETA1-4 : angle 1.44881 ( 6) link_NAG-ASN : bond 0.00045 ( 1) link_NAG-ASN : angle 3.42205 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.288 Fit side-chains REVERT: A 416 PHE cc_start: 0.7537 (m-80) cc_final: 0.7329 (m-10) REVERT: A 524 MET cc_start: 0.8008 (tpp) cc_final: 0.7781 (tpp) REVERT: A 543 MET cc_start: 0.8380 (mtp) cc_final: 0.8090 (mtp) REVERT: A 699 ASP cc_start: 0.8455 (t0) cc_final: 0.8222 (t0) REVERT: A 882 HIS cc_start: 0.7791 (m-70) cc_final: 0.6588 (p90) REVERT: A 908 LYS cc_start: 0.8374 (mmtm) cc_final: 0.8086 (mmmt) REVERT: A 942 HIS cc_start: 0.6925 (m-70) cc_final: 0.6307 (t-90) REVERT: B 63 ASP cc_start: 0.6869 (p0) cc_final: 0.6631 (p0) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.5001 time to fit residues: 70.0225 Evaluate side-chains 85 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS A 741 ASN A 841 GLN A 853 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114724 restraints weight = 12869.453| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.18 r_work: 0.3359 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7915 Z= 0.134 Angle : 0.564 6.658 10788 Z= 0.279 Chirality : 0.044 0.163 1143 Planarity : 0.005 0.044 1412 Dihedral : 9.393 75.232 1132 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.29 % Allowed : 9.16 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.28), residues: 944 helix: 1.74 (0.44), residues: 156 sheet: 0.40 (0.35), residues: 250 loop : -1.25 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 588 TYR 0.012 0.001 TYR A 257 PHE 0.010 0.001 PHE A 101 TRP 0.012 0.001 TRP A 503 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7907) covalent geometry : angle 0.55611 (10768) SS BOND : bond 0.00242 ( 4) SS BOND : angle 0.66578 ( 8) hydrogen bonds : bond 0.03835 ( 253) hydrogen bonds : angle 4.95792 ( 732) link_ALPHA1-3 : bond 0.01632 ( 1) link_ALPHA1-3 : angle 3.76896 ( 3) link_BETA1-4 : bond 0.00786 ( 2) link_BETA1-4 : angle 1.82830 ( 6) link_NAG-ASN : bond 0.00310 ( 1) link_NAG-ASN : angle 3.20039 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.201 Fit side-chains REVERT: A 107 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7869 (mp0) REVERT: A 416 PHE cc_start: 0.7543 (m-80) cc_final: 0.7303 (m-10) REVERT: A 489 TYR cc_start: 0.7759 (OUTLIER) cc_final: 0.6545 (m-80) REVERT: A 524 MET cc_start: 0.8025 (tpp) cc_final: 0.7821 (tpp) REVERT: A 561 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: A 588 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7419 (ttp80) REVERT: A 699 ASP cc_start: 0.8493 (t0) cc_final: 0.8261 (t0) REVERT: A 908 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8134 (mmmt) REVERT: A 942 HIS cc_start: 0.7431 (m-70) cc_final: 0.6485 (t-90) outliers start: 19 outliers final: 7 residues processed: 95 average time/residue: 0.4906 time to fit residues: 49.5251 Evaluate side-chains 83 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 918 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 87 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 0.0470 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 676 HIS A 741 ASN A 855 GLN B 76 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.129780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.115044 restraints weight = 12672.419| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.15 r_work: 0.3367 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7915 Z= 0.102 Angle : 0.524 7.031 10788 Z= 0.255 Chirality : 0.043 0.168 1143 Planarity : 0.004 0.039 1412 Dihedral : 6.845 56.607 1132 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.53 % Allowed : 10.12 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.28), residues: 944 helix: 2.14 (0.45), residues: 154 sheet: 0.43 (0.35), residues: 250 loop : -1.18 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 588 TYR 0.010 0.001 TYR A 257 PHE 0.011 0.001 PHE A 101 TRP 0.012 0.001 TRP A 503 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 7907) covalent geometry : angle 0.51755 (10768) SS BOND : bond 0.00189 ( 4) SS BOND : angle 0.52199 ( 8) hydrogen bonds : bond 0.03207 ( 253) hydrogen bonds : angle 4.58723 ( 732) link_ALPHA1-3 : bond 0.01978 ( 1) link_ALPHA1-3 : angle 3.26880 ( 3) link_BETA1-4 : bond 0.00648 ( 2) link_BETA1-4 : angle 1.67428 ( 6) link_NAG-ASN : bond 0.00158 ( 1) link_NAG-ASN : angle 2.89995 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.236 Fit side-chains REVERT: A 107 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7882 (mt-10) REVERT: A 416 PHE cc_start: 0.7587 (m-80) cc_final: 0.7339 (m-10) REVERT: A 489 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.6807 (m-80) REVERT: A 561 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7526 (pm20) REVERT: A 699 ASP cc_start: 0.8430 (t0) cc_final: 0.8193 (t0) REVERT: A 721 GLU cc_start: 0.8746 (tp30) cc_final: 0.8372 (mt-10) REVERT: A 908 LYS cc_start: 0.8370 (mmtm) cc_final: 0.8132 (mmmt) REVERT: A 942 HIS cc_start: 0.7412 (m-70) cc_final: 0.6469 (t-90) REVERT: B 56 CYS cc_start: 0.8128 (t) cc_final: 0.7772 (t) outliers start: 21 outliers final: 5 residues processed: 97 average time/residue: 0.4479 time to fit residues: 46.5532 Evaluate side-chains 81 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 918 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.0000 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS A 741 ASN A 855 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.110778 restraints weight = 12945.773| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.14 r_work: 0.3303 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7915 Z= 0.159 Angle : 0.580 7.393 10788 Z= 0.285 Chirality : 0.045 0.204 1143 Planarity : 0.004 0.043 1412 Dihedral : 5.756 43.006 1132 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.89 % Allowed : 10.84 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.28), residues: 944 helix: 2.01 (0.45), residues: 154 sheet: 0.36 (0.35), residues: 249 loop : -1.28 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 478 TYR 0.009 0.001 TYR A 477 PHE 0.011 0.001 PHE B 48 TRP 0.011 0.002 TRP A 503 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 7907) covalent geometry : angle 0.57333 (10768) SS BOND : bond 0.00279 ( 4) SS BOND : angle 0.66583 ( 8) hydrogen bonds : bond 0.03684 ( 253) hydrogen bonds : angle 4.68290 ( 732) link_ALPHA1-3 : bond 0.01989 ( 1) link_ALPHA1-3 : angle 3.46919 ( 3) link_BETA1-4 : bond 0.00673 ( 2) link_BETA1-4 : angle 1.65590 ( 6) link_NAG-ASN : bond 0.00049 ( 1) link_NAG-ASN : angle 3.34996 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.311 Fit side-chains REVERT: A 107 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7960 (mt-10) REVERT: A 377 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.7683 (mpp80) REVERT: A 416 PHE cc_start: 0.7693 (m-80) cc_final: 0.7354 (m-10) REVERT: A 561 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: A 699 ASP cc_start: 0.8510 (t0) cc_final: 0.8280 (t0) REVERT: B 54 ASP cc_start: 0.7912 (m-30) cc_final: 0.7540 (m-30) REVERT: B 56 CYS cc_start: 0.8034 (t) cc_final: 0.7801 (t) outliers start: 24 outliers final: 7 residues processed: 93 average time/residue: 0.4995 time to fit residues: 49.4305 Evaluate side-chains 82 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 918 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS A 741 ASN A 855 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.125776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.110895 restraints weight = 12925.928| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.28 r_work: 0.3310 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7915 Z= 0.141 Angle : 0.556 6.480 10788 Z= 0.273 Chirality : 0.044 0.201 1143 Planarity : 0.004 0.043 1412 Dihedral : 5.354 42.744 1132 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.65 % Allowed : 11.81 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.28), residues: 944 helix: 2.07 (0.45), residues: 154 sheet: 0.34 (0.35), residues: 246 loop : -1.27 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 309 TYR 0.008 0.001 TYR A 498 PHE 0.011 0.001 PHE B 48 TRP 0.012 0.001 TRP A 503 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 7907) covalent geometry : angle 0.55059 (10768) SS BOND : bond 0.00291 ( 4) SS BOND : angle 0.61683 ( 8) hydrogen bonds : bond 0.03452 ( 253) hydrogen bonds : angle 4.61450 ( 732) link_ALPHA1-3 : bond 0.01953 ( 1) link_ALPHA1-3 : angle 2.85666 ( 3) link_BETA1-4 : bond 0.00648 ( 2) link_BETA1-4 : angle 1.38202 ( 6) link_NAG-ASN : bond 0.00113 ( 1) link_NAG-ASN : angle 3.15290 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.322 Fit side-chains REVERT: A 72 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7453 (p0) REVERT: A 107 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7981 (mt-10) REVERT: A 154 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8171 (mtp-110) REVERT: A 228 GLU cc_start: 0.7045 (mp0) cc_final: 0.6773 (mp0) REVERT: A 416 PHE cc_start: 0.7703 (m-80) cc_final: 0.7415 (m-10) REVERT: A 424 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.8009 (m-30) REVERT: A 478 ARG cc_start: 0.5605 (OUTLIER) cc_final: 0.5365 (ttp80) REVERT: A 561 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7897 (pm20) REVERT: A 699 ASP cc_start: 0.8508 (t0) cc_final: 0.8274 (t0) REVERT: A 705 TYR cc_start: 0.8646 (m-80) cc_final: 0.8339 (m-10) REVERT: B 54 ASP cc_start: 0.7968 (m-30) cc_final: 0.7568 (m-30) outliers start: 22 outliers final: 7 residues processed: 93 average time/residue: 0.4972 time to fit residues: 49.1181 Evaluate side-chains 87 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 793 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 82 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 0.0670 chunk 83 optimal weight: 0.0170 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS A 741 ASN A 841 GLN A 855 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.112423 restraints weight = 12954.985| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.30 r_work: 0.3326 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7915 Z= 0.102 Angle : 0.532 7.528 10788 Z= 0.259 Chirality : 0.043 0.187 1143 Planarity : 0.004 0.041 1412 Dihedral : 4.973 40.199 1132 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.29 % Allowed : 12.53 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.28), residues: 944 helix: 2.20 (0.45), residues: 154 sheet: 0.36 (0.35), residues: 246 loop : -1.19 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 864 TYR 0.007 0.001 TYR A 257 PHE 0.011 0.001 PHE A 101 TRP 0.011 0.001 TRP A 503 HIS 0.002 0.001 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7907) covalent geometry : angle 0.52726 (10768) SS BOND : bond 0.00224 ( 4) SS BOND : angle 0.55527 ( 8) hydrogen bonds : bond 0.03094 ( 253) hydrogen bonds : angle 4.46656 ( 732) link_ALPHA1-3 : bond 0.01689 ( 1) link_ALPHA1-3 : angle 2.46059 ( 3) link_BETA1-4 : bond 0.00621 ( 2) link_BETA1-4 : angle 1.31002 ( 6) link_NAG-ASN : bond 0.00063 ( 1) link_NAG-ASN : angle 2.95327 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.296 Fit side-chains REVERT: A 54 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6966 (mmp-170) REVERT: A 107 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7996 (mt-10) REVERT: A 228 GLU cc_start: 0.6954 (mp0) cc_final: 0.6681 (mp0) REVERT: A 416 PHE cc_start: 0.7688 (m-80) cc_final: 0.7383 (m-10) REVERT: A 424 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: A 561 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: A 699 ASP cc_start: 0.8525 (t0) cc_final: 0.8288 (t0) REVERT: A 705 TYR cc_start: 0.8566 (m-80) cc_final: 0.8267 (m-10) REVERT: A 841 GLN cc_start: 0.8800 (tt0) cc_final: 0.8584 (tt0) REVERT: B 54 ASP cc_start: 0.7919 (m-30) cc_final: 0.7558 (m-30) outliers start: 19 outliers final: 6 residues processed: 96 average time/residue: 0.5159 time to fit residues: 52.7271 Evaluate side-chains 88 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ARG Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 715 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 480 HIS A 676 HIS A 678 HIS A 841 GLN A 855 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.106724 restraints weight = 12918.965| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.27 r_work: 0.3258 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 7915 Z= 0.255 Angle : 0.652 7.085 10788 Z= 0.325 Chirality : 0.048 0.185 1143 Planarity : 0.005 0.040 1412 Dihedral : 5.423 46.081 1132 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.13 % Allowed : 12.53 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.27), residues: 944 helix: 1.70 (0.44), residues: 154 sheet: 0.27 (0.35), residues: 240 loop : -1.38 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 864 TYR 0.014 0.002 TYR A 509 PHE 0.017 0.002 PHE B 48 TRP 0.014 0.002 TRP A 540 HIS 0.006 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00606 ( 7907) covalent geometry : angle 0.64812 (10768) SS BOND : bond 0.00404 ( 4) SS BOND : angle 0.81180 ( 8) hydrogen bonds : bond 0.04343 ( 253) hydrogen bonds : angle 4.90228 ( 732) link_ALPHA1-3 : bond 0.01739 ( 1) link_ALPHA1-3 : angle 2.01979 ( 3) link_BETA1-4 : bond 0.00582 ( 2) link_BETA1-4 : angle 1.42822 ( 6) link_NAG-ASN : bond 0.00118 ( 1) link_NAG-ASN : angle 3.57663 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.279 Fit side-chains REVERT: A 107 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7975 (mt-10) REVERT: A 228 GLU cc_start: 0.7063 (mp0) cc_final: 0.6716 (mp0) REVERT: A 253 MET cc_start: 0.8349 (mmt) cc_final: 0.8087 (mmm) REVERT: A 377 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.7848 (mpp80) REVERT: A 416 PHE cc_start: 0.7781 (m-80) cc_final: 0.7401 (m-10) REVERT: A 424 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: A 478 ARG cc_start: 0.5491 (OUTLIER) cc_final: 0.5239 (ttp80) REVERT: A 561 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7976 (pm20) REVERT: A 699 ASP cc_start: 0.8571 (t0) cc_final: 0.8321 (t0) REVERT: A 705 TYR cc_start: 0.8795 (m-80) cc_final: 0.8558 (m-10) REVERT: A 841 GLN cc_start: 0.8733 (tt0) cc_final: 0.8489 (tt0) REVERT: A 857 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7618 (mtm180) outliers start: 26 outliers final: 11 residues processed: 94 average time/residue: 0.6459 time to fit residues: 64.0448 Evaluate side-chains 89 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 857 ARG Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain B residue 67 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS A 678 HIS A 841 GLN A 855 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.123242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.108399 restraints weight = 12784.759| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.28 r_work: 0.3282 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7915 Z= 0.139 Angle : 0.574 7.506 10788 Z= 0.283 Chirality : 0.044 0.152 1143 Planarity : 0.004 0.041 1412 Dihedral : 5.126 44.128 1132 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.05 % Allowed : 13.86 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.28), residues: 944 helix: 1.96 (0.44), residues: 154 sheet: 0.23 (0.35), residues: 238 loop : -1.32 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 864 TYR 0.008 0.001 TYR A 509 PHE 0.011 0.001 PHE B 48 TRP 0.011 0.001 TRP A 540 HIS 0.005 0.001 HIS A 678 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7907) covalent geometry : angle 0.56970 (10768) SS BOND : bond 0.00297 ( 4) SS BOND : angle 0.64067 ( 8) hydrogen bonds : bond 0.03566 ( 253) hydrogen bonds : angle 4.69420 ( 732) link_ALPHA1-3 : bond 0.01443 ( 1) link_ALPHA1-3 : angle 1.88587 ( 3) link_BETA1-4 : bond 0.00715 ( 2) link_BETA1-4 : angle 1.35754 ( 6) link_NAG-ASN : bond 0.00055 ( 1) link_NAG-ASN : angle 3.23358 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.329 Fit side-chains REVERT: A 107 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7964 (mt-10) REVERT: A 228 GLU cc_start: 0.7036 (mp0) cc_final: 0.6679 (mp0) REVERT: A 253 MET cc_start: 0.8361 (mmt) cc_final: 0.8119 (mmm) REVERT: A 416 PHE cc_start: 0.7707 (m-80) cc_final: 0.7372 (m-10) REVERT: A 424 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: A 478 ARG cc_start: 0.5579 (OUTLIER) cc_final: 0.5283 (ttp80) REVERT: A 699 ASP cc_start: 0.8542 (t0) cc_final: 0.8278 (t0) REVERT: A 705 TYR cc_start: 0.8687 (m-80) cc_final: 0.8445 (m-10) REVERT: B 54 ASP cc_start: 0.7875 (m-30) cc_final: 0.7510 (m-30) outliers start: 17 outliers final: 8 residues processed: 88 average time/residue: 0.6159 time to fit residues: 57.4199 Evaluate side-chains 86 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 67 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.5671 > 50: distance: 3 - 20: 11.353 distance: 16 - 20: 8.730 distance: 20 - 21: 7.179 distance: 21 - 22: 18.133 distance: 21 - 24: 18.547 distance: 22 - 23: 12.314 distance: 22 - 26: 29.049 distance: 24 - 25: 22.347 distance: 26 - 27: 24.650 distance: 27 - 28: 29.454 distance: 27 - 30: 20.209 distance: 28 - 29: 5.896 distance: 28 - 34: 40.878 distance: 30 - 31: 20.075 distance: 30 - 32: 12.013 distance: 31 - 33: 15.738 distance: 34 - 35: 37.627 distance: 35 - 36: 28.089 distance: 35 - 38: 30.912 distance: 36 - 37: 54.839 distance: 36 - 45: 29.839 distance: 38 - 39: 18.229 distance: 39 - 40: 31.396 distance: 40 - 41: 17.810 distance: 41 - 42: 11.001 distance: 42 - 43: 9.407 distance: 42 - 44: 12.585 distance: 45 - 46: 26.884 distance: 45 - 51: 23.744 distance: 46 - 47: 43.631 distance: 46 - 49: 34.848 distance: 47 - 48: 16.666 distance: 47 - 52: 43.855 distance: 49 - 50: 70.567 distance: 50 - 51: 45.650 distance: 52 - 53: 25.116 distance: 53 - 54: 28.478 distance: 54 - 55: 40.875 distance: 54 - 56: 17.624 distance: 56 - 57: 8.422 distance: 57 - 58: 38.917 distance: 57 - 60: 33.633 distance: 58 - 59: 5.621 distance: 58 - 64: 42.115 distance: 60 - 61: 17.574 distance: 61 - 62: 8.850 distance: 61 - 63: 8.501 distance: 64 - 65: 24.007 distance: 65 - 66: 31.849 distance: 65 - 68: 29.333 distance: 66 - 67: 26.380 distance: 66 - 70: 12.342 distance: 68 - 69: 19.676 distance: 70 - 71: 21.773 distance: 70 - 76: 18.106 distance: 71 - 72: 18.848 distance: 71 - 74: 14.559 distance: 72 - 73: 4.525 distance: 72 - 77: 10.423 distance: 74 - 75: 9.902 distance: 75 - 76: 18.021 distance: 77 - 78: 18.299 distance: 78 - 79: 20.988 distance: 78 - 81: 21.091 distance: 79 - 80: 10.500 distance: 79 - 89: 13.352 distance: 81 - 82: 15.731 distance: 82 - 83: 21.551 distance: 82 - 84: 13.095 distance: 83 - 85: 6.781 distance: 84 - 86: 8.713 distance: 85 - 87: 15.355 distance: 86 - 87: 18.623 distance: 87 - 88: 12.223 distance: 89 - 90: 16.067 distance: 90 - 91: 18.720 distance: 90 - 93: 44.348 distance: 91 - 92: 7.450 distance: 91 - 100: 31.153 distance: 93 - 94: 44.990 distance: 94 - 95: 21.547 distance: 95 - 96: 11.113 distance: 96 - 97: 13.323 distance: 97 - 98: 4.767 distance: 97 - 99: 3.745