Starting phenix.real_space_refine on Thu Jul 2 22:44:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ny2_8996/07_2026/6ny2_8996.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ny2_8996/07_2026/6ny2_8996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ny2_8996/07_2026/6ny2_8996.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ny2_8996/07_2026/6ny2_8996.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ny2_8996/07_2026/6ny2_8996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ny2_8996/07_2026/6ny2_8996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ny2_8996/07_2026/6ny2_8996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ny2_8996/07_2026/6ny2_8996.map" } resolution = 3.2 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= 0.002 sd= 0.059 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 P 180 5.49 5 S 21 5.16 5 C 6035 2.51 5 N 1921 2.21 5 O 2381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10538 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 715 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "D" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 708 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "Y" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 829 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "Y" Number of atoms: 5055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5055 Classifications: {'peptide': 678} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 121} Link IDs: {'PTRANS': 22, 'TRANS': 655} Chain breaks: 5 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 468 Unresolved non-hydrogen dihedrals: 249 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 57, 'ASN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 15, 'GLU:plan': 23, 'ARG:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 237 Chain: "Y" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 887 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 64, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "B" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2344 Classifications: {'RNA': 110} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 45} Link IDs: {'rna2p': 10, 'rna3p': 99} Chain breaks: 2 Time building chain proxies: 2.30, per 1000 atoms: 0.22 Number of scatterers: 10538 At special positions: 0 Unit cell: (98.1, 140.4, 122.4, 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) S 21 16.00 P 180 15.00 O 2381 8.00 N 1921 7.00 C 6035 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS Y 826 " - pdb=" SG CYS Y 928 " 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 TRANS " UNK Y 104 " - " SER Y 103 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 254.3 milliseconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 47.4% alpha, 5.9% beta 64 base pairs and 114 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'Y' and resid 4 through 13 removed outlier: 3.833A pdb=" N ILE Y 8 " --> pdb=" O ARG Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 42 Processing helix chain 'Y' and resid 60 through 88 Processing helix chain 'Y' and resid 90 through 98 Processing helix chain 'Y' and resid 194 through 198 Processing helix chain 'Y' and resid 209 through 214 Processing helix chain 'Y' and resid 222 through 259 removed outlier: 4.249A pdb=" N ASP Y 245 " --> pdb=" O SER Y 241 " (cutoff:3.500A) Processing helix chain 'Y' and resid 262 through 271 Processing helix chain 'Y' and resid 287 through 308 Processing helix chain 'Y' and resid 342 through 357 removed outlier: 3.590A pdb=" N THR Y 346 " --> pdb=" O ASP Y 342 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS Y 357 " --> pdb=" O LEU Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 357 through 366 removed outlier: 3.616A pdb=" N GLY Y 361 " --> pdb=" O LYS Y 357 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL Y 363 " --> pdb=" O ASP Y 359 " (cutoff:3.500A) Processing helix chain 'Y' and resid 370 through 380 Processing helix chain 'Y' and resid 405 through 418 Processing helix chain 'Y' and resid 424 through 449 removed outlier: 3.545A pdb=" N GLU Y 428 " --> pdb=" O LYS Y 424 " (cutoff:3.500A) Processing helix chain 'Y' and resid 456 through 473 Processing helix chain 'Y' and resid 474 through 476 No H-bonds generated for 'chain 'Y' and resid 474 through 476' Processing helix chain 'Y' and resid 483 through 501 Processing helix chain 'Y' and resid 602 through 610 Processing helix chain 'Y' and resid 711 through 728 removed outlier: 4.368A pdb=" N ARG Y 728 " --> pdb=" O VAL Y 724 " (cutoff:3.500A) Processing helix chain 'Y' and resid 738 through 762 removed outlier: 3.757A pdb=" N HIS Y 762 " --> pdb=" O HIS Y 758 " (cutoff:3.500A) Processing helix chain 'Y' and resid 788 through 802 removed outlier: 3.663A pdb=" N MET Y 792 " --> pdb=" O GLN Y 788 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU Y 793 " --> pdb=" O TYR Y 789 " (cutoff:3.500A) Processing helix chain 'Y' and resid 886 through 893 Processing helix chain 'Y' and resid 897 through 903 Processing helix chain 'Y' and resid 906 through 914 removed outlier: 3.996A pdb=" N UNK Y 910 " --> pdb=" O UNK Y 906 " (cutoff:3.500A) Processing helix chain 'Y' and resid 935 through 950 removed outlier: 3.715A pdb=" N LEU Y 947 " --> pdb=" O ALA Y 943 " (cutoff:3.500A) Processing helix chain 'Y' and resid 965 through 981 removed outlier: 3.595A pdb=" N ALA Y 969 " --> pdb=" O PRO Y 965 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG Y 976 " --> pdb=" O ALA Y 972 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS Y 979 " --> pdb=" O LYS Y 975 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 18 through 20 Processing sheet with id=AA2, first strand: chain 'Y' and resid 27 through 29 removed outlier: 6.826A pdb=" N THR Y 651 " --> pdb=" O ALA Y 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 33 through 34 Processing sheet with id=AA4, first strand: chain 'Y' and resid 557 through 558 removed outlier: 3.596A pdb=" N ARG Y 557 " --> pdb=" O THR Y 586 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 633 through 634 removed outlier: 3.878A pdb=" N GLU Y 643 " --> pdb=" O ILE Y 634 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Y' and resid 669 through 670 removed outlier: 6.351A pdb=" N ILE Y 669 " --> pdb=" O VAL Y 767 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ALA Y 769 " --> pdb=" O ILE Y 669 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Y' and resid 923 through 924 removed outlier: 3.587A pdb=" N VAL Y 932 " --> pdb=" O PHE Y 923 " (cutoff:3.500A) 285 hydrogen bonds defined for protein. 837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 156 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 114 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1893 1.33 - 1.45: 3610 1.45 - 1.57: 5213 1.57 - 1.69: 355 1.69 - 1.82: 34 Bond restraints: 11105 Sorted by residual: bond pdb=" C1' DT C 6 " pdb=" N1 DT C 6 " ideal model delta sigma weight residual 1.468 1.527 -0.059 1.40e-02 5.10e+03 1.77e+01 bond pdb=" N1 DC C 13 " pdb=" C6 DC C 13 " ideal model delta sigma weight residual 1.367 1.342 0.025 6.00e-03 2.78e+04 1.72e+01 bond pdb=" C3' DG C 12 " pdb=" O3' DG C 12 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.51e+01 bond pdb=" C4' DC C 10 " pdb=" C3' DC C 10 " ideal model delta sigma weight residual 1.529 1.491 0.038 1.00e-02 1.00e+04 1.42e+01 bond pdb=" C1' DC D 28 " pdb=" N1 DC D 28 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.23e+01 ... (remaining 11100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 15512 2.92 - 5.84: 293 5.84 - 8.76: 39 8.76 - 11.68: 6 11.68 - 14.60: 1 Bond angle restraints: 15851 Sorted by residual: angle pdb=" O4' DC D 24 " pdb=" C1' DC D 24 " pdb=" N1 DC D 24 " ideal model delta sigma weight residual 108.00 113.10 -5.10 7.00e-01 2.04e+00 5.30e+01 angle pdb=" N SER Y 197 " pdb=" CA SER Y 197 " pdb=" C SER Y 197 " ideal model delta sigma weight residual 114.64 104.07 10.57 1.52e+00 4.33e-01 4.84e+01 angle pdb=" N GLY Y 572 " pdb=" CA GLY Y 572 " pdb=" C GLY Y 572 " ideal model delta sigma weight residual 113.18 127.78 -14.60 2.37e+00 1.78e-01 3.79e+01 angle pdb=" C ILE Y 198 " pdb=" N HIS Y 199 " pdb=" CA HIS Y 199 " ideal model delta sigma weight residual 121.54 133.12 -11.58 1.91e+00 2.74e-01 3.68e+01 angle pdb=" CA TRP Y 534 " pdb=" CB TRP Y 534 " pdb=" CG TRP Y 534 " ideal model delta sigma weight residual 113.60 124.37 -10.77 1.90e+00 2.77e-01 3.21e+01 ... (remaining 15846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.26: 5753 34.26 - 68.51: 436 68.51 - 102.77: 28 102.77 - 137.03: 1 137.03 - 171.29: 4 Dihedral angle restraints: 6222 sinusoidal: 3565 harmonic: 2657 Sorted by residual: dihedral pdb=" O4' U B 17 " pdb=" C1' U B 17 " pdb=" N1 U B 17 " pdb=" C2 U B 17 " ideal model delta sinusoidal sigma weight residual 232.00 60.71 171.29 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" CA ILE Y 198 " pdb=" C ILE Y 198 " pdb=" N HIS Y 199 " pdb=" CA HIS Y 199 " ideal model delta harmonic sigma weight residual -180.00 -142.36 -37.64 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CA GLY Y 367 " pdb=" C GLY Y 367 " pdb=" N VAL Y 368 " pdb=" CA VAL Y 368 " ideal model delta harmonic sigma weight residual 180.00 -144.29 -35.71 0 5.00e+00 4.00e-02 5.10e+01 ... (remaining 6219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1534 0.066 - 0.133: 289 0.133 - 0.199: 44 0.199 - 0.265: 8 0.265 - 0.331: 5 Chirality restraints: 1880 Sorted by residual: chirality pdb=" C3' C B 40 " pdb=" C4' C B 40 " pdb=" O3' C B 40 " pdb=" C2' C B 40 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C3' G B 44 " pdb=" C4' G B 44 " pdb=" O3' G B 44 " pdb=" C2' G B 44 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C3' G B 60 " pdb=" C4' G B 60 " pdb=" O3' G B 60 " pdb=" C2' G B 60 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1877 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN Y 501 " 0.052 5.00e-02 4.00e+02 7.88e-02 9.94e+00 pdb=" N PRO Y 502 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO Y 502 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO Y 502 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE Y 609 " -0.021 2.00e-02 2.50e+03 1.95e-02 6.64e+00 pdb=" CG PHE Y 609 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE Y 609 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE Y 609 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE Y 609 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE Y 609 " -0.017 2.00e-02 2.50e+03 pdb=" CZ PHE Y 609 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 56 " 0.033 2.00e-02 2.50e+03 1.53e-02 6.40e+00 pdb=" N9 A B 56 " -0.035 2.00e-02 2.50e+03 pdb=" C8 A B 56 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A B 56 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A B 56 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A B 56 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A B 56 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A B 56 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A B 56 " -0.010 2.00e-02 2.50e+03 pdb=" N3 A B 56 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A B 56 " -0.002 2.00e-02 2.50e+03 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2526 2.79 - 3.32: 8775 3.32 - 3.85: 19254 3.85 - 4.37: 21458 4.37 - 4.90: 32711 Nonbonded interactions: 84724 Sorted by model distance: nonbonded pdb=" OH TYR Y 196 " pdb=" O SER Y 221 " model vdw 2.266 3.040 nonbonded pdb=" OG1 THR Y 684 " pdb=" O ASP Y 685 " model vdw 2.268 3.040 nonbonded pdb=" O SER Y 738 " pdb=" OG SER Y 738 " model vdw 2.297 3.040 nonbonded pdb=" OG1 THR Y 603 " pdb=" OP2 A B 18 " model vdw 2.306 3.040 nonbonded pdb=" ND2 ASN Y 549 " pdb=" O GLY Y 554 " model vdw 2.308 3.120 ... (remaining 84719 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: 1.560 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.740 Find NCS groups from input model: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.007 0.073 11107 Z= 0.474 Angle : 1.048 14.600 15856 Z= 0.663 Chirality : 0.057 0.331 1880 Planarity : 0.007 0.079 1379 Dihedral : 20.326 171.287 4492 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.77 % Allowed : 15.60 % Favored : 83.63 % Rotamer: Outliers : 0.66 % Allowed : 8.39 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -4.66 (0.23), residues: 782 helix: -2.21 (0.20), residues: 344 sheet: -2.39 (0.59), residues: 84 loop : -4.25 (0.23), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Y 673 TYR 0.018 0.003 TYR Y 818 PHE 0.042 0.003 PHE Y 609 TRP 0.035 0.002 TRP Y 534 HIS 0.015 0.002 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00746 / 0.47 (11105) covalent geometry : angle 1.04753 / 0.66 (15851) SS BOND : bond 0.00116 / 0.06 ( 1) SS BOND : angle 1.71962 / 1.67 ( 2) hydrogen bonds : bond 0.13859 / 15.03 ( 441) hydrogen bonds : angle 6.64515 / 7.92 ( 1131) link_TRANS : bond 0.00044 / 0.02 ( 1) link_TRANS : angle 0.93798 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 302 MET cc_start: 0.7905 (ttp) cc_final: 0.7688 (ttm) REVERT: Y 778 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8164 (tm-30) outliers start: 4 outliers final: 2 residues processed: 86 average time/residue: 0.1465 time to fit residues: 16.2370 Evaluate side-chains 60 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 583 ILE Chi-restraints excluded: chain Y residue 684 THR 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: 0.7980 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.116823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.087183 restraints weight = 22511.628| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.27 r_work: 0.3244 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11107 Z= 0.168 Angle : 0.758 11.017 15856 Z= 0.409 Chirality : 0.043 0.232 1880 Planarity : 0.005 0.042 1379 Dihedral : 21.512 172.138 3055 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.96 % Favored : 84.78 % Rotamer: Outliers : 1.81 % Allowed : 13.16 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.26 % 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 are not related in a simple way. whole: -3.19 (0.27), residues: 782 helix: -0.44 (0.26), residues: 354 sheet: -2.07 (0.62), residues: 76 loop : -4.06 (0.25), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Y 777 TYR 0.020 0.002 TYR Y 575 PHE 0.026 0.002 PHE Y 609 TRP 0.032 0.001 TRP Y 534 HIS 0.006 0.001 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.17 (11105) covalent geometry : angle 0.75781 / 0.41 (15851) SS BOND : bond 0.00033 / 0.02 ( 1) SS BOND : angle 1.05077 / 0.70 ( 2) hydrogen bonds : bond 0.06064 / 6.39 ( 441) hydrogen bonds : angle 4.62937 / 5.71 ( 1131) link_TRANS : bond 0.00064 / 0.03 ( 1) link_TRANS : angle 0.81275 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: Y 573 LEU cc_start: 0.8917 (tp) cc_final: 0.8706 (tt) REVERT: Y 778 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8203 (tm-30) REVERT: Y 784 MET cc_start: 0.8844 (mmm) cc_final: 0.7987 (mmm) REVERT: Y 812 SER cc_start: 0.8602 (t) cc_final: 0.8270 (p) outliers start: 11 outliers final: 6 residues processed: 83 average time/residue: 0.1124 time to fit residues: 13.2050 Evaluate side-chains 65 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 967 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.117393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087608 restraints weight = 22828.068| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.30 r_work: 0.3256 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11107 Z= 0.159 Angle : 0.707 9.823 15856 Z= 0.383 Chirality : 0.041 0.226 1880 Planarity : 0.004 0.038 1379 Dihedral : 21.460 174.144 3053 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.83 % Favored : 85.04 % Rotamer: Outliers : 2.63 % Allowed : 16.94 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 are not related in a simple way. whole: -2.51 (0.29), residues: 782 helix: 0.32 (0.28), residues: 355 sheet: -2.10 (0.62), residues: 78 loop : -3.87 (0.26), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 773 TYR 0.012 0.001 TYR Y 818 PHE 0.025 0.002 PHE Y 609 TRP 0.024 0.001 TRP Y 534 HIS 0.004 0.001 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (11105) covalent geometry : angle 0.70677 / 0.38 (15851) SS BOND : bond 0.00074 / 0.04 ( 1) SS BOND : angle 0.86939 / 0.78 ( 2) hydrogen bonds : bond 0.05529 / 5.89 ( 441) hydrogen bonds : angle 4.34015 / 5.33 ( 1131) link_TRANS : bond 0.00057 / 0.03 ( 1) link_TRANS : angle 0.58809 / 0.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: Y 265 ARG cc_start: 0.8439 (tmm-80) cc_final: 0.8157 (tmm-80) REVERT: Y 778 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8208 (tm-30) REVERT: Y 784 MET cc_start: 0.8917 (mmm) cc_final: 0.7974 (mmm) REVERT: Y 812 SER cc_start: 0.8673 (t) cc_final: 0.8305 (p) REVERT: Y 970 TRP cc_start: 0.8174 (t60) cc_final: 0.7583 (t60) outliers start: 16 outliers final: 11 residues processed: 81 average time/residue: 0.0922 time to fit residues: 11.0459 Evaluate side-chains 72 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 583 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 949 LEU Chi-restraints excluded: chain Y residue 967 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 12 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 56 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.116907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087249 restraints weight = 22756.915| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.29 r_work: 0.3249 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11107 Z= 0.177 Angle : 0.702 9.542 15856 Z= 0.379 Chirality : 0.041 0.223 1880 Planarity : 0.004 0.038 1379 Dihedral : 21.450 172.945 3053 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.60 % Favored : 84.27 % Rotamer: Outliers : 2.47 % Allowed : 18.91 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 are not related in a simple way. whole: -2.13 (0.30), residues: 782 helix: 0.69 (0.28), residues: 355 sheet: -2.07 (0.62), residues: 79 loop : -3.69 (0.27), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 917 TYR 0.011 0.001 TYR Y 818 PHE 0.022 0.002 PHE Y 609 TRP 0.028 0.001 TRP Y 534 HIS 0.004 0.001 HIS Y 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.18 (11105) covalent geometry : angle 0.70172 / 0.38 (15851) SS BOND : bond 0.00004 / 0.00 ( 1) SS BOND : angle 0.68592 / 0.66 ( 2) hydrogen bonds : bond 0.05396 / 5.74 ( 441) hydrogen bonds : angle 4.19123 / 5.16 ( 1131) link_TRANS : bond 0.00056 / 0.03 ( 1) link_TRANS : angle 0.85985 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: Y 265 ARG cc_start: 0.8454 (tmm-80) cc_final: 0.8191 (tmm-80) REVERT: Y 778 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8228 (tm-30) REVERT: Y 784 MET cc_start: 0.8891 (mmm) cc_final: 0.8020 (mmm) REVERT: Y 970 TRP cc_start: 0.8169 (t60) cc_final: 0.7482 (t60) outliers start: 15 outliers final: 11 residues processed: 75 average time/residue: 0.0973 time to fit residues: 10.7694 Evaluate side-chains 72 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 583 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 967 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 77 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 90 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 35 optimal weight: 0.1980 chunk 24 optimal weight: 0.0370 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.118472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.088912 restraints weight = 22801.597| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.31 r_work: 0.3287 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11107 Z= 0.142 Angle : 0.667 9.182 15856 Z= 0.359 Chirality : 0.040 0.223 1880 Planarity : 0.004 0.035 1379 Dihedral : 21.440 176.106 3053 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.83 % Favored : 85.17 % Rotamer: Outliers : 2.80 % Allowed : 18.59 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.30), residues: 782 helix: 0.91 (0.29), residues: 355 sheet: -2.10 (0.61), residues: 79 loop : -3.49 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 654 TYR 0.028 0.001 TYR Y 575 PHE 0.018 0.002 PHE Y 609 TRP 0.023 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (11105) covalent geometry : angle 0.66695 / 0.36 (15851) SS BOND : bond 0.00046 / 0.02 ( 1) SS BOND : angle 0.74006 / 0.59 ( 2) hydrogen bonds : bond 0.05070 / 5.34 ( 441) hydrogen bonds : angle 4.06132 / 4.99 ( 1131) link_TRANS : bond 0.00031 / 0.02 ( 1) link_TRANS : angle 0.78253 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.306 Fit side-chains REVERT: Y 265 ARG cc_start: 0.8437 (tmm-80) cc_final: 0.8235 (tmm-80) REVERT: Y 736 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7183 (p90) REVERT: Y 778 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8138 (tm-30) REVERT: Y 784 MET cc_start: 0.8858 (mmm) cc_final: 0.7991 (mmm) REVERT: Y 812 SER cc_start: 0.8652 (t) cc_final: 0.8341 (p) REVERT: Y 970 TRP cc_start: 0.8156 (t60) cc_final: 0.7472 (t60) outliers start: 17 outliers final: 12 residues processed: 88 average time/residue: 0.0988 time to fit residues: 12.6894 Evaluate side-chains 77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 583 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 683 LEU Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 736 PHE Chi-restraints excluded: chain Y residue 932 VAL Chi-restraints excluded: chain Y residue 949 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 0.0670 chunk 88 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 overall best weight: 1.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.117094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.087444 restraints weight = 22920.951| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.35 r_work: 0.3267 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11107 Z= 0.164 Angle : 0.674 8.875 15856 Z= 0.364 Chirality : 0.040 0.220 1880 Planarity : 0.004 0.034 1379 Dihedral : 21.386 174.485 3053 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.22 % Favored : 84.65 % Rotamer: Outliers : 3.29 % Allowed : 18.91 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.30), residues: 782 helix: 1.05 (0.29), residues: 355 sheet: -2.11 (0.60), residues: 79 loop : -3.40 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 66 TYR 0.010 0.001 TYR Y 818 PHE 0.018 0.001 PHE Y 609 TRP 0.026 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (11105) covalent geometry : angle 0.67410 / 0.36 (15851) SS BOND : bond 0.00012 / 0.01 ( 1) SS BOND : angle 0.56741 / 0.63 ( 2) hydrogen bonds : bond 0.05101 / 5.38 ( 441) hydrogen bonds : angle 4.02403 / 4.93 ( 1131) link_TRANS : bond 0.00048 / 0.02 ( 1) link_TRANS : angle 0.92996 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.302 Fit side-chains REVERT: Y 736 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7412 (p90) REVERT: Y 778 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8129 (tm-30) REVERT: Y 784 MET cc_start: 0.8895 (mmm) cc_final: 0.8004 (mmm) REVERT: Y 794 ASP cc_start: 0.8452 (m-30) cc_final: 0.8226 (m-30) REVERT: Y 812 SER cc_start: 0.8644 (t) cc_final: 0.8352 (p) REVERT: Y 970 TRP cc_start: 0.8157 (t60) cc_final: 0.7436 (t60) outliers start: 20 outliers final: 12 residues processed: 85 average time/residue: 0.1024 time to fit residues: 12.7902 Evaluate side-chains 77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 425 VAL Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 736 PHE Chi-restraints excluded: chain Y residue 932 VAL Chi-restraints excluded: chain Y residue 967 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 23 optimal weight: 7.9990 chunk 4 optimal weight: 50.0000 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.115372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085304 restraints weight = 22642.240| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.29 r_work: 0.3224 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11107 Z= 0.220 Angle : 0.717 9.506 15856 Z= 0.385 Chirality : 0.042 0.223 1880 Planarity : 0.005 0.045 1379 Dihedral : 21.383 169.858 3053 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.11 % Favored : 83.76 % Rotamer: Outliers : 2.96 % Allowed : 19.74 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.31), residues: 782 helix: 1.12 (0.29), residues: 355 sheet: -2.43 (0.59), residues: 83 loop : -3.37 (0.28), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 66 TYR 0.009 0.002 TYR Y 818 PHE 0.019 0.002 PHE Y 609 TRP 0.027 0.001 TRP Y 534 HIS 0.004 0.001 HIS Y 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.22 (11105) covalent geometry : angle 0.71712 / 0.39 (15851) SS BOND : bond 0.00038 / 0.02 ( 1) SS BOND : angle 0.60959 / 0.58 ( 2) hydrogen bonds : bond 0.05435 / 5.77 ( 441) hydrogen bonds : angle 4.04216 / 4.94 ( 1131) link_TRANS : bond 0.00118 / 0.06 ( 1) link_TRANS : angle 0.82641 / 0.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.296 Fit side-chains REVERT: Y 736 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.7146 (p90) REVERT: Y 778 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8072 (tm-30) REVERT: Y 784 MET cc_start: 0.8786 (mmm) cc_final: 0.8063 (mmm) REVERT: Y 970 TRP cc_start: 0.8211 (t60) cc_final: 0.7440 (t60) outliers start: 18 outliers final: 15 residues processed: 76 average time/residue: 0.0876 time to fit residues: 10.2041 Evaluate side-chains 72 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 302 MET Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 531 LEU Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 736 PHE Chi-restraints excluded: chain Y residue 932 VAL Chi-restraints excluded: chain Y residue 967 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 83 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 71 optimal weight: 0.1980 chunk 17 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.116855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.087077 restraints weight = 22472.886| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.29 r_work: 0.3248 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11107 Z= 0.170 Angle : 0.686 9.232 15856 Z= 0.369 Chirality : 0.041 0.221 1880 Planarity : 0.004 0.045 1379 Dihedral : 21.417 172.708 3053 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.22 % Favored : 84.65 % Rotamer: Outliers : 3.12 % Allowed : 19.74 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.31), residues: 782 helix: 1.14 (0.29), residues: 356 sheet: -2.23 (0.60), residues: 79 loop : -3.32 (0.28), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Y 66 TYR 0.011 0.001 TYR Y 818 PHE 0.015 0.002 PHE Y 609 TRP 0.027 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (11105) covalent geometry : angle 0.68628 / 0.37 (15851) SS BOND : bond 0.00031 / 0.02 ( 1) SS BOND : angle 0.61972 / 0.65 ( 2) hydrogen bonds : bond 0.05166 / 5.47 ( 441) hydrogen bonds : angle 4.01281 / 4.91 ( 1131) link_TRANS : bond 0.00085 / 0.04 ( 1) link_TRANS : angle 1.08728 / 0.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.314 Fit side-chains REVERT: Y 736 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7127 (p90) REVERT: Y 778 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8101 (tm-30) REVERT: Y 784 MET cc_start: 0.8756 (mmm) cc_final: 0.7954 (mmm) REVERT: Y 970 TRP cc_start: 0.8206 (t60) cc_final: 0.7458 (t60) outliers start: 19 outliers final: 13 residues processed: 81 average time/residue: 0.0816 time to fit residues: 10.3498 Evaluate side-chains 71 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 736 PHE Chi-restraints excluded: chain Y residue 807 SER Chi-restraints excluded: chain Y residue 932 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 88 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.117333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.087697 restraints weight = 22472.868| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.34 r_work: 0.3269 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11107 Z= 0.152 Angle : 0.678 8.681 15856 Z= 0.363 Chirality : 0.040 0.220 1880 Planarity : 0.004 0.048 1379 Dihedral : 21.381 174.836 3053 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.09 % Favored : 84.91 % Rotamer: Outliers : 2.30 % Allowed : 20.56 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.31), residues: 782 helix: 1.20 (0.29), residues: 356 sheet: -2.20 (0.62), residues: 78 loop : -3.22 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Y 66 TYR 0.011 0.001 TYR Y 818 PHE 0.016 0.002 PHE Y 775 TRP 0.022 0.001 TRP Y 534 HIS 0.002 0.001 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (11105) covalent geometry : angle 0.67834 / 0.36 (15851) SS BOND : bond 0.00053 / 0.03 ( 1) SS BOND : angle 0.69603 / 0.61 ( 2) hydrogen bonds : bond 0.04986 / 5.26 ( 441) hydrogen bonds : angle 3.94637 / 4.81 ( 1131) link_TRANS : bond 0.00071 / 0.04 ( 1) link_TRANS : angle 1.01189 / 0.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.325 Fit side-chains REVERT: Y 338 GLU cc_start: 0.7731 (pt0) cc_final: 0.7488 (tm-30) REVERT: Y 530 ASN cc_start: 0.8896 (m-40) cc_final: 0.8696 (m-40) REVERT: Y 736 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7318 (p90) REVERT: Y 778 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8128 (tm-30) REVERT: Y 784 MET cc_start: 0.8787 (mmm) cc_final: 0.7989 (mmm) REVERT: Y 812 SER cc_start: 0.8675 (t) cc_final: 0.8356 (p) REVERT: Y 970 TRP cc_start: 0.8181 (t60) cc_final: 0.7584 (t60) outliers start: 14 outliers final: 11 residues processed: 82 average time/residue: 0.0926 time to fit residues: 11.5409 Evaluate side-chains 75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 736 PHE Chi-restraints excluded: chain Y residue 932 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.858 > 50: distance: 47 - 52: 35.075 distance: 52 - 53: 42.891 distance: 53 - 54: 46.637 distance: 53 - 56: 23.122 distance: 54 - 55: 69.296 distance: 54 - 57: 56.607 distance: 57 - 58: 70.275 distance: 59 - 60: 55.185 distance: 59 - 64: 38.170 distance: 61 - 62: 41.241 distance: 62 - 63: 54.589 distance: 64 - 65: 40.379 distance: 65 - 66: 39.805 distance: 65 - 68: 40.406 distance: 66 - 67: 39.172 distance: 69 - 70: 68.799 distance: 70 - 71: 18.952 distance: 71 - 72: 58.262 distance: 71 - 73: 42.983 distance: 74 - 75: 39.624 distance: 75 - 76: 55.567 distance: 75 - 79: 40.326 distance: 77 - 78: 55.083 distance: 79 - 80: 49.514 distance: 80 - 81: 42.257 distance: 80 - 83: 48.060 distance: 81 - 82: 44.099 distance: 83 - 84: 40.664 distance: 84 - 85: 69.437 distance: 86 - 87: 58.414 distance: 87 - 88: 10.163 distance: 87 - 90: 55.238 distance: 88 - 89: 57.709 distance: 88 - 94: 55.861 distance: 90 - 91: 55.410 distance: 91 - 92: 45.086 distance: 91 - 93: 57.870 distance: 94 - 95: 15.670 distance: 95 - 96: 49.916 distance: 95 - 98: 54.945 distance: 96 - 97: 39.359 distance: 96 - 105: 39.968 distance: 98 - 99: 40.703 distance: 99 - 100: 69.055 distance: 100 - 101: 45.660 distance: 101 - 102: 39.905 distance: 102 - 103: 19.183 distance: 102 - 104: 33.605 distance: 105 - 106: 61.070 distance: 106 - 107: 43.683 distance: 106 - 109: 23.259 distance: 107 - 108: 57.716 distance: 107 - 113: 65.065 distance: 109 - 110: 57.303 distance: 109 - 111: 49.629 distance: 110 - 112: 38.802 distance: 113 - 114: 29.596 distance: 114 - 115: 9.954 distance: 115 - 116: 38.897 distance: 115 - 117: 35.447