Starting phenix.real_space_refine on Fri Sep 11 17:45:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ny2_8996/09_2026/6ny2_8996.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ny2_8996/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ny2_8996/09_2026/6ny2_8996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ny2_8996/09_2026/6ny2_8996.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ny2_8996/09_2026/6ny2_8996.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ny2_8996/09_2026/6ny2_8996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ny2_8996/09_2026/6ny2_8996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ny2_8996/09_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-2.2.1-6174/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: {'RNAv2': 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: 1.94, per 1000 atoms: 0.18 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: 0.86 Conformation dependent library (CDL) restraints added in 229.8 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: 1.30 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: 2.77 Time building geometry restraints manager: 1.12 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: 15386 2.92 - 5.84: 415 5.84 - 8.76: 43 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=" C3' C B 40 " pdb=" O3' C B 40 " pdb=" P U B 41 " ideal model delta sigma weight residual 119.70 126.92 -7.22 1.20e+00 6.94e-01 3.62e+01 ... (remaining 15846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.56: 5495 29.56 - 59.11: 658 59.11 - 88.67: 65 88.67 - 118.22: 0 118.22 - 147.78: 4 Dihedral angle restraints: 6222 sinusoidal: 3565 harmonic: 2657 Sorted by residual: dihedral pdb=" C4' U B 16 " pdb=" C3' U B 16 " pdb=" C2' U B 16 " pdb=" C1' U B 16 " ideal model delta sinusoidal sigma weight residual 36.34 -37.79 74.13 1 3.10e+00 1.04e-01 7.26e+02 dihedral pdb=" C4' A B 49 " pdb=" C3' A B 49 " pdb=" C2' A B 49 " pdb=" C1' A B 49 " ideal model delta sinusoidal sigma weight residual 36.34 -36.84 73.19 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' U B 17 " pdb=" C3' U B 17 " pdb=" C2' U B 17 " pdb=" C1' U B 17 " ideal model delta sinusoidal sigma weight residual 36.35 -36.58 72.92 1 3.10e+00 1.04e-01 7.06e+02 ... (remaining 6219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1535 0.084 - 0.167: 192 0.167 - 0.251: 122 0.251 - 0.335: 28 0.335 - 0.418: 3 Chirality restraints: 1880 Sorted by residual: chirality pdb=" P U B 41 " pdb=" OP1 U B 41 " pdb=" OP2 U B 41 " pdb=" O5' U B 41 " both_signs ideal model delta sigma weight residual True 2.17 -2.59 -0.42 2.00e-01 2.50e+01 4.38e+00 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 -2.50 -2.15 -0.35 2.00e-01 2.50e+01 3.11e+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 -2.50 -2.16 -0.34 2.00e-01 2.50e+01 2.90e+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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.610 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.300 ------------------------------------------------------------------------------- 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 : 0.008 0.073 11107 Z= 0.473 Angle : 1.124 14.600 15856 Z= 0.666 Chirality : 0.083 0.418 1880 Planarity : 0.007 0.079 1379 Dihedral : 21.682 147.777 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 0.00754 / 0.47 (11105) covalent geometry : angle 1.12345 / 0.67 (15851) SS BOND : bond 0.00116 / 0.06 ( 1) SS BOND : angle 1.71962 / 1.67 ( 2) hydrogen bonds : bond 0.13859 / 15.07 ( 441) hydrogen bonds : angle 6.64515 / 7.91 ( 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 : 0.299 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: 0.1447 time to fit residues: 16.1153 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 : 0.297 ------------------------------------------------------------------------------- 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: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.117362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.087653 restraints weight = 22527.839| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.27 r_work: 0.3252 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11107 Z= 0.207 Angle : 1.119 22.306 15856 Z= 0.501 Chirality : 0.096 1.507 1880 Planarity : 0.005 0.042 1379 Dihedral : 22.342 152.996 3055 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.96 % Favored : 84.78 % Rotamer: Outliers : 2.14 % Allowed : 13.32 % Favored : 84.54 % 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: -3.17 (0.27), residues: 782 helix: -0.41 (0.26), residues: 354 sheet: -2.07 (0.62), residues: 76 loop : -4.07 (0.25), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Y 777 TYR 0.021 0.002 TYR Y 575 PHE 0.026 0.002 PHE Y 609 TRP 0.032 0.002 TRP Y 534 HIS 0.007 0.001 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.21 (11105) covalent geometry : angle 1.11865 / 0.50 (15851) SS BOND : bond 0.00006 / 0.00 ( 1) SS BOND : angle 1.07990 / 0.72 ( 2) hydrogen bonds : bond 0.05900 / 6.31 ( 441) hydrogen bonds : angle 4.62116 / 5.70 ( 1131) link_TRANS : bond 0.00056 / 0.03 ( 1) link_TRANS : angle 0.81080 / 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 83 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: Y 573 LEU cc_start: 0.8928 (tp) cc_final: 0.8719 (tt) REVERT: Y 778 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8228 (tm-30) REVERT: Y 784 MET cc_start: 0.8833 (mmm) cc_final: 0.7979 (mmm) outliers start: 13 outliers final: 7 residues processed: 78 average time/residue: 0.0927 time to fit residues: 10.4165 Evaluate side-chains 64 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 574 LEU 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: 3.9990 chunk 3 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 55 optimal weight: 0.0870 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 overall best weight: 1.5562 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.117556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.087833 restraints weight = 22893.376| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.24 r_work: 0.3263 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11107 Z= 0.189 Angle : 0.934 11.131 15856 Z= 0.438 Chirality : 0.068 0.904 1880 Planarity : 0.005 0.040 1379 Dihedral : 22.425 161.567 3053 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.22 % Favored : 84.65 % Rotamer: Outliers : 2.96 % Allowed : 16.94 % Favored : 80.10 % 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: -2.62 (0.29), residues: 782 helix: 0.26 (0.28), residues: 355 sheet: -2.38 (0.60), residues: 82 loop : -3.89 (0.25), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Y 773 TYR 0.015 0.001 TYR Y 575 PHE 0.025 0.002 PHE Y 609 TRP 0.025 0.002 TRP Y 534 HIS 0.004 0.001 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (11105) covalent geometry : angle 0.93442 / 0.44 (15851) SS BOND : bond 0.00031 / 0.02 ( 1) SS BOND : angle 0.86960 / 0.71 ( 2) hydrogen bonds : bond 0.05687 / 6.18 ( 441) hydrogen bonds : angle 4.35832 / 5.35 ( 1131) link_TRANS : bond 0.00044 / 0.02 ( 1) link_TRANS : angle 0.65393 / 0.45 ( 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 82 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: Y 265 ARG cc_start: 0.8427 (tmm-80) cc_final: 0.8157 (tmm-80) REVERT: Y 313 LYS cc_start: 0.8081 (mmmt) cc_final: 0.7657 (mtpt) REVERT: Y 778 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8271 (tm-30) REVERT: Y 784 MET cc_start: 0.8914 (mmm) cc_final: 0.7986 (mmm) REVERT: Y 970 TRP cc_start: 0.8154 (t60) cc_final: 0.7613 (t60) outliers start: 18 outliers final: 9 residues processed: 78 average time/residue: 0.0836 time to fit residues: 9.7337 Evaluate side-chains 69 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 368 VAL 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: 3.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 89 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.120363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.090805 restraints weight = 22791.290| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.31 r_work: 0.3315 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11107 Z= 0.153 Angle : 0.876 10.839 15856 Z= 0.410 Chirality : 0.062 0.548 1880 Planarity : 0.004 0.038 1379 Dihedral : 22.242 164.063 3053 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.96 % Favored : 85.04 % Rotamer: Outliers : 2.30 % Allowed : 17.60 % Favored : 80.10 % 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: -2.14 (0.30), residues: 782 helix: 0.67 (0.28), residues: 355 sheet: -2.30 (0.61), residues: 82 loop : -3.61 (0.28), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 777 TYR 0.017 0.001 TYR Y 575 PHE 0.025 0.002 PHE Y 503 TRP 0.026 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (11105) covalent geometry : angle 0.87555 / 0.41 (15851) SS BOND : bond 0.00022 / 0.01 ( 1) SS BOND : angle 0.73866 / 0.66 ( 2) hydrogen bonds : bond 0.05225 / 5.61 ( 441) hydrogen bonds : angle 4.20248 / 5.20 ( 1131) link_TRANS : bond 0.00035 / 0.02 ( 1) link_TRANS : angle 0.82036 / 0.63 ( 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 87 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: Y 265 ARG cc_start: 0.8422 (tmm-80) cc_final: 0.8176 (tmm-80) REVERT: Y 778 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8216 (tm-30) REVERT: Y 784 MET cc_start: 0.8880 (mmm) cc_final: 0.8054 (mmm) REVERT: Y 812 SER cc_start: 0.8634 (t) cc_final: 0.8332 (p) REVERT: Y 970 TRP cc_start: 0.8120 (t60) cc_final: 0.7509 (t60) outliers start: 14 outliers final: 10 residues processed: 85 average time/residue: 0.0937 time to fit residues: 11.6096 Evaluate side-chains 75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 42 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.117798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.088265 restraints weight = 22887.121| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.29 r_work: 0.3269 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2059 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= 0.213 Angle : 0.890 10.469 15856 Z= 0.418 Chirality : 0.061 0.547 1880 Planarity : 0.005 0.041 1379 Dihedral : 22.165 165.489 3053 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.83 % Favored : 84.91 % Rotamer: Outliers : 3.12 % Allowed : 18.91 % Favored : 77.96 % 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: -1.96 (0.30), residues: 782 helix: 0.88 (0.29), residues: 355 sheet: -2.41 (0.59), residues: 83 loop : -3.55 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Y 917 TYR 0.010 0.002 TYR Y 818 PHE 0.020 0.002 PHE Y 609 TRP 0.023 0.001 TRP Y 534 HIS 0.004 0.001 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.21 (11105) covalent geometry : angle 0.89045 / 0.42 (15851) SS BOND : bond 0.00032 / 0.02 ( 1) SS BOND : angle 0.62578 / 0.71 ( 2) hydrogen bonds : bond 0.05492 / 5.96 ( 441) hydrogen bonds : angle 4.11185 / 5.06 ( 1131) link_TRANS : bond 0.00068 / 0.03 ( 1) link_TRANS : angle 0.79000 / 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 85 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.303 Fit side-chains REVERT: Y 736 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7026 (p90) REVERT: Y 778 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8124 (tm-30) REVERT: Y 784 MET cc_start: 0.8928 (mmm) cc_final: 0.7936 (mmm) REVERT: Y 970 TRP cc_start: 0.8186 (t60) cc_final: 0.7428 (t60) outliers start: 19 outliers final: 13 residues processed: 83 average time/residue: 0.0851 time to fit residues: 10.5635 Evaluate side-chains 76 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain Y residue 949 LEU Chi-restraints excluded: chain Y residue 967 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.118404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.088818 restraints weight = 22788.348| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.30 r_work: 0.3282 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11107 Z= 0.181 Angle : 0.867 10.260 15856 Z= 0.407 Chirality : 0.060 0.502 1880 Planarity : 0.004 0.035 1379 Dihedral : 22.142 166.690 3053 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.58 % Favored : 85.29 % Rotamer: Outliers : 3.62 % Allowed : 19.41 % Favored : 76.97 % 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: -1.81 (0.30), residues: 782 helix: 1.00 (0.29), residues: 355 sheet: -2.47 (0.59), residues: 83 loop : -3.42 (0.28), residues: 344 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 0.021 0.002 PHE Y 775 TRP 0.028 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (11105) covalent geometry : angle 0.86669 / 0.41 (15851) SS BOND : bond 0.00015 / 0.01 ( 1) SS BOND : angle 0.62590 / 0.66 ( 2) hydrogen bonds : bond 0.05261 / 5.68 ( 441) hydrogen bonds : angle 4.08103 / 5.02 ( 1131) link_TRANS : bond 0.00076 / 0.04 ( 1) link_TRANS : angle 0.98078 / 0.78 ( 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 86 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.306 Fit side-chains REVERT: Y 736 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7180 (p90) REVERT: Y 778 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8143 (tm-30) REVERT: Y 784 MET cc_start: 0.8872 (mmm) cc_final: 0.7963 (mmm) REVERT: Y 970 TRP cc_start: 0.8214 (t60) cc_final: 0.7488 (t60) outliers start: 22 outliers final: 16 residues processed: 82 average time/residue: 0.0827 time to fit residues: 10.5787 Evaluate side-chains 77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 683 LEU Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 736 PHE Chi-restraints excluded: chain Y residue 782 THR Chi-restraints excluded: chain Y residue 807 SER 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: 6.9990 chunk 4 optimal weight: 40.0000 chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 0.0050 chunk 17 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.120659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.091186 restraints weight = 22529.404| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.29 r_work: 0.3340 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11107 Z= 0.146 Angle : 0.833 10.165 15856 Z= 0.391 Chirality : 0.058 0.436 1880 Planarity : 0.004 0.047 1379 Dihedral : 22.074 168.244 3053 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 2.30 % Allowed : 20.39 % 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: -1.59 (0.31), residues: 782 helix: 1.19 (0.29), residues: 353 sheet: -2.13 (0.62), residues: 78 loop : -3.34 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Y 66 TYR 0.018 0.001 TYR Y 711 PHE 0.021 0.002 PHE Y 775 TRP 0.018 0.001 TRP Y 534 HIS 0.002 0.001 HIS Y 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (11105) covalent geometry : angle 0.83263 / 0.39 (15851) SS BOND : bond 0.00023 / 0.01 ( 1) SS BOND : angle 0.72717 / 0.67 ( 2) hydrogen bonds : bond 0.05049 / 5.42 ( 441) hydrogen bonds : angle 3.99721 / 4.94 ( 1131) link_TRANS : bond 0.00044 / 0.02 ( 1) link_TRANS : angle 0.83435 / 0.69 ( 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 91 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.202 Fit side-chains REVERT: Y 31 LEU cc_start: 0.8303 (tp) cc_final: 0.7438 (tp) REVERT: Y 313 LYS cc_start: 0.8383 (mmmt) cc_final: 0.7841 (mmtt) REVERT: Y 778 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8066 (tm-30) REVERT: Y 784 MET cc_start: 0.8554 (mmm) cc_final: 0.7884 (mmm) REVERT: Y 812 SER cc_start: 0.8683 (t) cc_final: 0.8424 (p) REVERT: Y 970 TRP cc_start: 0.8161 (t60) cc_final: 0.7609 (t60) outliers start: 14 outliers final: 10 residues processed: 89 average time/residue: 0.0860 time to fit residues: 11.4036 Evaluate side-chains 71 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 639 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 782 THR Chi-restraints excluded: chain Y residue 932 VAL Chi-restraints excluded: chain Y residue 949 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 83 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 71 optimal weight: 0.0970 chunk 17 optimal weight: 9.9990 chunk 24 optimal weight: 0.0570 chunk 3 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.2302 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.118480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.088751 restraints weight = 22563.850| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.30 r_work: 0.3283 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11107 Z= 0.208 Angle : 0.866 9.389 15856 Z= 0.406 Chirality : 0.059 0.468 1880 Planarity : 0.004 0.041 1379 Dihedral : 22.033 168.345 3053 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.96 % Favored : 84.78 % Rotamer: Outliers : 2.14 % Allowed : 21.22 % Favored : 76.64 % 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: -1.65 (0.31), residues: 782 helix: 1.11 (0.29), residues: 355 sheet: -2.43 (0.59), residues: 82 loop : -3.30 (0.29), residues: 345 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 0.032 0.002 PHE Y 484 TRP 0.028 0.001 TRP Y 534 HIS 0.004 0.001 HIS Y 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.21 (11105) covalent geometry : angle 0.86600 / 0.41 (15851) SS BOND : bond 0.00002 / 0.00 ( 1) SS BOND : angle 0.47661 / 0.64 ( 2) hydrogen bonds : bond 0.05312 / 5.72 ( 441) hydrogen bonds : angle 4.02936 / 4.98 ( 1131) link_TRANS : bond 0.00113 / 0.06 ( 1) link_TRANS : angle 1.14602 / 0.93 ( 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 75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.183 Fit side-chains REVERT: Y 736 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7294 (p90) REVERT: Y 778 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8127 (tm-30) REVERT: Y 784 MET cc_start: 0.8701 (mmm) cc_final: 0.7917 (mmm) REVERT: Y 970 TRP cc_start: 0.8190 (t60) cc_final: 0.7471 (t60) outliers start: 13 outliers final: 10 residues processed: 73 average time/residue: 0.0687 time to fit residues: 7.7853 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 : 0.237 ------------------------------------------------------------------------------- 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 639 ILE 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 765 VAL Chi-restraints excluded: chain Y residue 782 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 88 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 16 optimal weight: 20.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.120912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.091262 restraints weight = 22555.054| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.28 r_work: 0.3328 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11107 Z= 0.149 Angle : 0.829 9.205 15856 Z= 0.389 Chirality : 0.057 0.430 1880 Planarity : 0.004 0.044 1379 Dihedral : 22.032 168.916 3053 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % Rotamer: Outliers : 2.14 % Allowed : 21.38 % Favored : 76.48 % 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: -1.58 (0.31), residues: 782 helix: 1.21 (0.29), residues: 355 sheet: -2.53 (0.57), residues: 89 loop : -3.28 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 66 TYR 0.011 0.001 TYR Y 818 PHE 0.030 0.002 PHE Y 484 TRP 0.024 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (11105) covalent geometry : angle 0.82922 / 0.39 (15851) SS BOND : bond 0.00008 / 0.00 ( 1) SS BOND : angle 0.62227 / 0.41 ( 2) hydrogen bonds : bond 0.05028 / 5.37 ( 441) hydrogen bonds : angle 3.95567 / 4.91 ( 1131) link_TRANS : bond 0.00042 / 0.02 ( 1) link_TRANS : angle 1.05196 / 0.87 ( 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 75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.308 Fit side-chains REVERT: Y 31 LEU cc_start: 0.8367 (tp) cc_final: 0.8010 (tp) REVERT: Y 736 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7471 (p90) REVERT: Y 778 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8082 (tm-30) REVERT: Y 784 MET cc_start: 0.8656 (mmm) cc_final: 0.7902 (mmm) REVERT: Y 970 TRP cc_start: 0.8131 (t60) cc_final: 0.7593 (t60) outliers start: 13 outliers final: 11 residues processed: 73 average time/residue: 0.0746 time to fit residues: 8.6092 Evaluate side-chains 74 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 736 PHE Chi-restraints excluded: chain Y residue 765 VAL Chi-restraints excluded: chain Y residue 782 THR Chi-restraints excluded: chain Y residue 932 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.118725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.089030 restraints weight = 22582.340| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.30 r_work: 0.3286 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11107 Z= 0.196 Angle : 0.855 8.959 15856 Z= 0.400 Chirality : 0.058 0.452 1880 Planarity : 0.004 0.038 1379 Dihedral : 21.998 168.591 3053 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.96 % Favored : 84.78 % Rotamer: Outliers : 2.47 % Allowed : 21.38 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.55 (0.31), residues: 782 helix: 1.20 (0.29), residues: 355 sheet: -2.35 (0.61), residues: 82 loop : -3.27 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 66 TYR 0.010 0.001 TYR Y 818 PHE 0.028 0.002 PHE Y 484 TRP 0.025 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.20 (11105) covalent geometry : angle 0.85464 / 0.40 (15851) SS BOND : bond 0.00033 / 0.02 ( 1) SS BOND : angle 0.51692 / 0.68 ( 2) hydrogen bonds : bond 0.05254 / 5.65 ( 441) hydrogen bonds : angle 3.97083 / 4.91 ( 1131) link_TRANS : bond 0.00068 / 0.03 ( 1) link_TRANS : angle 1.10252 / 0.92 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 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 77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.297 Fit side-chains REVERT: Y 31 LEU cc_start: 0.8528 (tp) cc_final: 0.8182 (tp) REVERT: Y 736 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7281 (p90) REVERT: Y 778 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8126 (tm-30) REVERT: Y 784 MET cc_start: 0.8746 (mmm) cc_final: 0.7883 (mmm) REVERT: Y 970 TRP cc_start: 0.8184 (t60) cc_final: 0.7549 (t60) outliers start: 15 outliers final: 13 residues processed: 74 average time/residue: 0.0800 time to fit residues: 9.2651 Evaluate side-chains 72 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 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 765 VAL Chi-restraints excluded: chain Y residue 782 THR Chi-restraints excluded: chain Y residue 932 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 37 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 71 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.121052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.091546 restraints weight = 22667.580| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.34 r_work: 0.3331 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11107 Z= 0.144 Angle : 0.823 8.771 15856 Z= 0.385 Chirality : 0.056 0.411 1880 Planarity : 0.004 0.040 1379 Dihedral : 21.979 169.114 3053 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.09 % Favored : 84.91 % Rotamer: Outliers : 2.47 % Allowed : 21.05 % Favored : 76.48 % 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: -1.48 (0.31), residues: 782 helix: 1.34 (0.29), residues: 353 sheet: -2.54 (0.60), residues: 85 loop : -3.23 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 66 TYR 0.010 0.001 TYR Y 818 PHE 0.029 0.002 PHE Y 484 TRP 0.024 0.001 TRP Y 534 HIS 0.002 0.001 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (11105) covalent geometry : angle 0.82279 / 0.38 (15851) SS BOND : bond 0.00232 / 0.12 ( 1) SS BOND : angle 0.69374 / 0.50 ( 2) hydrogen bonds : bond 0.04959 / 5.31 ( 441) hydrogen bonds : angle 3.88972 / 4.82 ( 1131) link_TRANS : bond 0.00010 / 0.01 ( 1) link_TRANS : angle 1.10964 / 0.94 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2260.56 seconds wall clock time: 39 minutes 29.19 seconds (2369.19 seconds total)