Starting phenix.real_space_refine on Wed Mar 4 04:03:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ny2_8996/03_2026/6ny2_8996.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ny2_8996/03_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_8996/03_2026/6ny2_8996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ny2_8996/03_2026/6ny2_8996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ny2_8996/03_2026/6ny2_8996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ny2_8996/03_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 2.52, per 1000 atoms: 0.24 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: 0.94 Conformation dependent library (CDL) restraints added in 324.7 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: 1.50 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: 2.43 Time building geometry restraints manager: 1.24 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=" C ASN Y 501 " pdb=" N PRO Y 502 " ideal model delta sigma weight residual 1.334 1.355 -0.021 8.40e-03 1.42e+04 6.32e+00 bond pdb=" CA LEU Y 615 " pdb=" CB LEU Y 615 " ideal model delta sigma weight residual 1.531 1.457 0.073 3.28e-02 9.30e+02 5.00e+00 bond pdb=" CA THR Y 782 " pdb=" CB THR Y 782 " ideal model delta sigma weight residual 1.526 1.497 0.030 1.53e-02 4.27e+03 3.75e+00 bond pdb=" CG1 ILE Y 79 " pdb=" CD1 ILE Y 79 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.86e+00 bond pdb=" C THR Y 279 " pdb=" N LEU Y 280 " ideal model delta sigma weight residual 1.331 1.296 0.035 2.07e-02 2.33e+03 2.82e+00 ... (remaining 11100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 15524 2.92 - 5.84: 281 5.84 - 8.76: 39 8.76 - 11.68: 6 11.68 - 14.60: 1 Bond angle restraints: 15851 Sorted by residual: 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 angle pdb=" C SER Y 772 " pdb=" N ARG Y 773 " pdb=" CA ARG Y 773 " ideal model delta sigma weight residual 121.31 129.16 -7.85 1.49e+00 4.50e-01 2.77e+01 ... (remaining 15846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.26: 5926 34.26 - 68.51: 598 68.51 - 102.77: 53 102.77 - 137.03: 1 137.03 - 171.29: 4 Dihedral angle restraints: 6582 sinusoidal: 3925 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 6579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1566 0.066 - 0.133: 259 0.133 - 0.199: 44 0.199 - 0.265: 6 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: 1.600 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.670 Find NCS groups from input model: 0.060 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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= 0.331 Angle : 1.015 14.600 15856 Z= 0.557 Chirality : 0.055 0.331 1880 Planarity : 0.007 0.079 1379 Dihedral : 22.805 171.287 4852 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 covalent geometry : bond 0.00704 (11105) covalent geometry : angle 1.01526 (15851) SS BOND : bond 0.00116 ( 1) SS BOND : angle 1.71962 ( 2) hydrogen bonds : bond 0.13859 ( 441) hydrogen bonds : angle 6.64515 ( 1131) link_TRANS : bond 0.00044 ( 1) link_TRANS : angle 0.93798 ( 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 : 0.213 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: 0.1672 time to fit residues: 18.4120 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 : 0.304 ------------------------------------------------------------------------------- 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: 6.9990 chunk 33 optimal weight: 3.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.118121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.088587 restraints weight = 22463.453| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.30 r_work: 0.3269 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11107 Z= 0.154 Angle : 0.704 9.894 15856 Z= 0.373 Chirality : 0.039 0.221 1880 Planarity : 0.005 0.041 1379 Dihedral : 24.354 174.119 3415 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.45 % Favored : 85.42 % Rotamer: Outliers : 2.47 % Allowed : 12.66 % Favored : 84.87 % 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: -2.98 (0.28), residues: 782 helix: -0.22 (0.26), residues: 353 sheet: -2.17 (0.62), residues: 78 loop : -3.94 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Y 324 TYR 0.011 0.001 TYR Y 818 PHE 0.031 0.002 PHE Y 503 TRP 0.028 0.001 TRP Y 534 HIS 0.006 0.001 HIS Y 250 Details of bonding type rmsd covalent geometry : bond 0.00316 (11105) covalent geometry : angle 0.70366 (15851) SS BOND : bond 0.00023 ( 1) SS BOND : angle 0.94653 ( 2) hydrogen bonds : bond 0.05444 ( 441) hydrogen bonds : angle 4.30910 ( 1131) link_TRANS : bond 0.00017 ( 1) link_TRANS : angle 0.54378 ( 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 93 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 86 GLU cc_start: 0.8623 (tp30) cc_final: 0.8382 (tp30) REVERT: Y 778 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8291 (tm-30) REVERT: Y 784 MET cc_start: 0.8876 (mmm) cc_final: 0.8211 (mmm) REVERT: Y 812 SER cc_start: 0.8703 (t) cc_final: 0.8404 (p) REVERT: Y 956 PHE cc_start: 0.7384 (t80) cc_final: 0.7134 (t80) REVERT: Y 970 TRP cc_start: 0.8189 (t60) cc_final: 0.7597 (t60) outliers start: 15 outliers final: 8 residues processed: 88 average time/residue: 0.1209 time to fit residues: 14.9117 Evaluate side-chains 70 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 683 LEU Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 807 SER 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: 1.9990 chunk 31 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.118951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.089539 restraints weight = 22751.775| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.33 r_work: 0.3294 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1948 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= 0.144 Angle : 0.657 8.183 15856 Z= 0.353 Chirality : 0.038 0.222 1880 Planarity : 0.004 0.039 1379 Dihedral : 24.279 176.043 3413 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.83 % Favored : 85.17 % Rotamer: Outliers : 3.12 % Allowed : 15.62 % Favored : 81.25 % 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: -2.19 (0.30), residues: 782 helix: 0.61 (0.28), residues: 355 sheet: -2.13 (0.62), residues: 78 loop : -3.68 (0.27), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 265 TYR 0.012 0.001 TYR Y 575 PHE 0.019 0.002 PHE Y 609 TRP 0.023 0.001 TRP Y 534 HIS 0.005 0.001 HIS Y 91 Details of bonding type rmsd covalent geometry : bond 0.00297 (11105) covalent geometry : angle 0.65680 (15851) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.80739 ( 2) hydrogen bonds : bond 0.04975 ( 441) hydrogen bonds : angle 4.05904 ( 1131) link_TRANS : bond 0.00068 ( 1) link_TRANS : angle 0.82180 ( 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 88 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.340 Fit side-chains REVERT: Y 86 GLU cc_start: 0.8649 (tp30) cc_final: 0.8244 (tm-30) REVERT: Y 778 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8200 (tm-30) REVERT: Y 784 MET cc_start: 0.8904 (mmm) cc_final: 0.8263 (mmm) REVERT: Y 812 SER cc_start: 0.8629 (t) cc_final: 0.8393 (p) REVERT: Y 970 TRP cc_start: 0.8186 (t60) cc_final: 0.7515 (t60) outliers start: 19 outliers final: 13 residues processed: 84 average time/residue: 0.0966 time to fit residues: 11.8603 Evaluate side-chains 73 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 91 HIS 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 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 765 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 12 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 23 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.119479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.090385 restraints weight = 22664.711| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.36 r_work: 0.3316 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11107 Z= 0.134 Angle : 0.639 8.209 15856 Z= 0.343 Chirality : 0.037 0.229 1880 Planarity : 0.004 0.035 1379 Dihedral : 24.200 177.117 3413 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.45 % Favored : 85.55 % Rotamer: Outliers : 2.96 % Allowed : 17.60 % Favored : 79.44 % 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: -1.74 (0.30), residues: 782 helix: 1.04 (0.29), residues: 356 sheet: -2.05 (0.62), residues: 78 loop : -3.49 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 734 TYR 0.010 0.001 TYR Y 818 PHE 0.015 0.001 PHE Y 609 TRP 0.023 0.001 TRP Y 534 HIS 0.018 0.002 HIS Y 91 Details of bonding type rmsd covalent geometry : bond 0.00274 (11105) covalent geometry : angle 0.63860 (15851) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.65329 ( 2) hydrogen bonds : bond 0.04733 ( 441) hydrogen bonds : angle 3.91977 ( 1131) link_TRANS : bond 0.00031 ( 1) link_TRANS : angle 0.90529 ( 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 92 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.287 Fit side-chains REVERT: Y 47 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7255 (mtp-110) REVERT: Y 86 GLU cc_start: 0.8654 (tp30) cc_final: 0.8265 (tm-30) REVERT: Y 778 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8136 (tm-30) REVERT: Y 784 MET cc_start: 0.8841 (mmm) cc_final: 0.8078 (mmm) REVERT: Y 812 SER cc_start: 0.8679 (t) cc_final: 0.8457 (p) REVERT: Y 970 TRP cc_start: 0.8180 (t60) cc_final: 0.7534 (t60) outliers start: 18 outliers final: 10 residues processed: 87 average time/residue: 0.1099 time to fit residues: 13.6525 Evaluate side-chains 73 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 67 MET 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 574 LEU 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 807 SER Chi-restraints excluded: chain Y residue 932 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 77 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.120398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.091032 restraints weight = 22848.495| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.40 r_work: 0.3326 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11107 Z= 0.133 Angle : 0.629 7.922 15856 Z= 0.335 Chirality : 0.036 0.220 1880 Planarity : 0.004 0.051 1379 Dihedral : 24.107 176.604 3413 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.22 % Favored : 84.78 % Rotamer: Outliers : 2.80 % Allowed : 18.91 % Favored : 78.29 % 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: -1.40 (0.31), residues: 782 helix: 1.31 (0.29), residues: 356 sheet: -1.95 (0.63), residues: 78 loop : -3.26 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 265 TYR 0.009 0.001 TYR Y 818 PHE 0.012 0.001 PHE Y 775 TRP 0.020 0.001 TRP Y 534 HIS 0.004 0.001 HIS Y 443 Details of bonding type rmsd covalent geometry : bond 0.00274 (11105) covalent geometry : angle 0.62845 (15851) SS BOND : bond 0.00065 ( 1) SS BOND : angle 0.62786 ( 2) hydrogen bonds : bond 0.04577 ( 441) hydrogen bonds : angle 3.77126 ( 1131) link_TRANS : bond 0.00046 ( 1) link_TRANS : angle 1.29845 ( 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 87 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.290 Fit side-chains REVERT: Y 47 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7276 (mtp-110) REVERT: Y 86 GLU cc_start: 0.8716 (tp30) cc_final: 0.8314 (tm-30) REVERT: Y 736 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.7656 (p90) REVERT: Y 778 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8095 (tm-30) REVERT: Y 784 MET cc_start: 0.8805 (mmm) cc_final: 0.8186 (mmm) REVERT: Y 812 SER cc_start: 0.8674 (t) cc_final: 0.8438 (p) REVERT: Y 970 TRP cc_start: 0.8175 (t60) cc_final: 0.7471 (t60) outliers start: 17 outliers final: 11 residues processed: 84 average time/residue: 0.0933 time to fit residues: 11.5331 Evaluate side-chains 79 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 91 HIS 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 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 807 SER Chi-restraints excluded: chain Y residue 932 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 34 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 82 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 0.0020 chunk 55 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.122588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.093824 restraints weight = 22945.551| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.41 r_work: 0.3377 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11107 Z= 0.122 Angle : 0.610 7.851 15856 Z= 0.326 Chirality : 0.036 0.220 1880 Planarity : 0.004 0.046 1379 Dihedral : 24.022 179.899 3413 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.43 % Favored : 86.57 % Rotamer: Outliers : 2.96 % Allowed : 19.90 % 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: -1.18 (0.32), residues: 782 helix: 1.57 (0.29), residues: 352 sheet: -2.20 (0.63), residues: 77 loop : -3.11 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 673 TYR 0.009 0.001 TYR Y 711 PHE 0.025 0.001 PHE Y 775 TRP 0.019 0.001 TRP Y 534 HIS 0.005 0.001 HIS Y 443 Details of bonding type rmsd covalent geometry : bond 0.00247 (11105) covalent geometry : angle 0.61024 (15851) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.61543 ( 2) hydrogen bonds : bond 0.04424 ( 441) hydrogen bonds : angle 3.67887 ( 1131) link_TRANS : bond 0.00122 ( 1) link_TRANS : angle 1.01210 ( 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 99 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.293 Fit side-chains REVERT: Y 47 ARG cc_start: 0.7798 (ttm-80) cc_final: 0.7262 (mtp180) REVERT: Y 86 GLU cc_start: 0.8663 (tp30) cc_final: 0.8316 (tm-30) REVERT: Y 447 GLU cc_start: 0.8430 (tp30) cc_final: 0.8103 (tp30) REVERT: Y 778 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8310 (tm-30) REVERT: Y 784 MET cc_start: 0.8714 (mmm) cc_final: 0.8066 (mmm) REVERT: Y 970 TRP cc_start: 0.8104 (t60) cc_final: 0.7504 (t60) outliers start: 18 outliers final: 12 residues processed: 94 average time/residue: 0.1046 time to fit residues: 13.8856 Evaluate side-chains 82 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 35 MET Chi-restraints excluded: chain Y residue 91 HIS Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 368 VAL 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 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 807 SER Chi-restraints excluded: chain Y residue 932 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.115838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.085841 restraints weight = 22718.575| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.33 r_work: 0.3225 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11107 Z= 0.245 Angle : 0.725 10.336 15856 Z= 0.383 Chirality : 0.041 0.223 1880 Planarity : 0.004 0.041 1379 Dihedral : 24.117 169.490 3413 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.96 % Favored : 84.78 % Rotamer: Outliers : 3.29 % Allowed : 20.23 % 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: -1.41 (0.31), residues: 782 helix: 1.36 (0.29), residues: 356 sheet: -2.20 (0.61), residues: 78 loop : -3.28 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 265 TYR 0.012 0.002 TYR Y 818 PHE 0.031 0.002 PHE Y 775 TRP 0.026 0.002 TRP Y 534 HIS 0.007 0.001 HIS Y 199 Details of bonding type rmsd covalent geometry : bond 0.00531 (11105) covalent geometry : angle 0.72536 (15851) SS BOND : bond 0.00079 ( 1) SS BOND : angle 0.38060 ( 2) hydrogen bonds : bond 0.05385 ( 441) hydrogen bonds : angle 3.88638 ( 1131) link_TRANS : bond 0.00100 ( 1) link_TRANS : angle 1.11111 ( 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 82 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.310 Fit side-chains REVERT: Y 47 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7302 (mtp-110) REVERT: Y 463 ASP cc_start: 0.8379 (m-30) cc_final: 0.8168 (m-30) REVERT: Y 557 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7921 (mtp180) REVERT: Y 736 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.7382 (p90) REVERT: Y 778 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8176 (tm-30) REVERT: Y 784 MET cc_start: 0.8678 (mmm) cc_final: 0.8028 (mmm) REVERT: Y 970 TRP cc_start: 0.8272 (t60) cc_final: 0.7386 (t60) outliers start: 20 outliers final: 15 residues processed: 77 average time/residue: 0.1019 time to fit residues: 11.4553 Evaluate side-chains 76 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 91 HIS Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE 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 557 ARG 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 807 SER Chi-restraints excluded: chain Y residue 812 SER Chi-restraints excluded: chain Y residue 932 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: 10.0000 chunk 71 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 24 optimal weight: 0.0030 chunk 3 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.115392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085437 restraints weight = 22700.957| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.32 r_work: 0.3216 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11107 Z= 0.241 Angle : 0.722 9.995 15856 Z= 0.382 Chirality : 0.041 0.223 1880 Planarity : 0.004 0.044 1379 Dihedral : 24.131 170.697 3413 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.60 % Favored : 84.27 % Rotamer: Outliers : 3.29 % Allowed : 20.56 % 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: -1.59 (0.31), residues: 782 helix: 1.20 (0.28), residues: 361 sheet: -2.66 (0.59), residues: 83 loop : -3.32 (0.28), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 673 TYR 0.012 0.002 TYR Y 818 PHE 0.035 0.002 PHE Y 775 TRP 0.026 0.002 TRP Y 534 HIS 0.004 0.001 HIS Y 199 Details of bonding type rmsd covalent geometry : bond 0.00520 (11105) covalent geometry : angle 0.72170 (15851) SS BOND : bond 0.00111 ( 1) SS BOND : angle 0.37367 ( 2) hydrogen bonds : bond 0.05412 ( 441) hydrogen bonds : angle 3.94606 ( 1131) link_TRANS : bond 0.00116 ( 1) link_TRANS : angle 1.14857 ( 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 78 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.304 Fit side-chains REVERT: Y 557 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7867 (mtp180) REVERT: Y 736 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.7092 (p90) REVERT: Y 778 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8242 (tm-30) REVERT: Y 784 MET cc_start: 0.8908 (mmm) cc_final: 0.8065 (mmm) REVERT: Y 970 TRP cc_start: 0.8251 (t60) cc_final: 0.7397 (t60) outliers start: 20 outliers final: 12 residues processed: 73 average time/residue: 0.0959 time to fit residues: 10.6026 Evaluate side-chains 70 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 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 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 557 ARG 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 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: 9.9990 chunk 27 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.119667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.090379 restraints weight = 22542.438| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.32 r_work: 0.3306 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2828 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= 0.136 Angle : 0.655 8.306 15856 Z= 0.346 Chirality : 0.037 0.218 1880 Planarity : 0.004 0.046 1379 Dihedral : 24.004 177.473 3413 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % Rotamer: Outliers : 2.14 % Allowed : 20.56 % 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: -1.25 (0.31), residues: 782 helix: 1.51 (0.29), residues: 356 sheet: -2.54 (0.60), residues: 83 loop : -3.08 (0.29), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 777 TYR 0.009 0.001 TYR Y 818 PHE 0.034 0.002 PHE Y 775 TRP 0.024 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 199 Details of bonding type rmsd covalent geometry : bond 0.00282 (11105) covalent geometry : angle 0.65497 (15851) SS BOND : bond 0.00038 ( 1) SS BOND : angle 0.61532 ( 2) hydrogen bonds : bond 0.04690 ( 441) hydrogen bonds : angle 3.77618 ( 1131) link_TRANS : bond 0.00048 ( 1) link_TRANS : angle 1.13433 ( 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 79 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.300 Fit side-chains REVERT: Y 31 LEU cc_start: 0.8337 (tp) cc_final: 0.7996 (tp) REVERT: Y 557 ARG cc_start: 0.8070 (mtp180) cc_final: 0.7856 (mtp180) REVERT: Y 736 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7694 (p90) REVERT: Y 778 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8183 (tm-30) REVERT: Y 784 MET cc_start: 0.8829 (mmm) cc_final: 0.8202 (mmm) REVERT: Y 970 TRP cc_start: 0.8199 (t60) cc_final: 0.7595 (t60) outliers start: 13 outliers final: 11 residues processed: 76 average time/residue: 0.0997 time to fit residues: 11.1937 Evaluate side-chains 70 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 368 VAL 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 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 807 SER 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: 0.5980 chunk 31 optimal weight: 0.0170 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 36 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 53 optimal weight: 0.0570 chunk 73 optimal weight: 2.9990 overall best weight: 0.1734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.125935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.097699 restraints weight = 22884.224| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.43 r_work: 0.3445 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11107 Z= 0.121 Angle : 0.629 7.919 15856 Z= 0.331 Chirality : 0.036 0.210 1880 Planarity : 0.004 0.046 1379 Dihedral : 23.889 174.055 3413 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.19 % Favored : 85.81 % Rotamer: Outliers : 1.64 % Allowed : 21.55 % Favored : 76.81 % 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: -0.98 (0.32), residues: 782 helix: 1.72 (0.29), residues: 352 sheet: -2.05 (0.66), residues: 77 loop : -2.98 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 265 TYR 0.009 0.001 TYR Y 545 PHE 0.032 0.001 PHE Y 775 TRP 0.019 0.001 TRP Y 611 HIS 0.009 0.001 HIS Y 443 Details of bonding type rmsd covalent geometry : bond 0.00245 (11105) covalent geometry : angle 0.62927 (15851) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.96650 ( 2) hydrogen bonds : bond 0.04446 ( 441) hydrogen bonds : angle 3.66107 ( 1131) link_TRANS : bond 0.00196 ( 1) link_TRANS : angle 1.06840 ( 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 92 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.304 Fit side-chains REVERT: Y 47 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7303 (mtp-110) REVERT: Y 72 TYR cc_start: 0.8121 (t80) cc_final: 0.7608 (t80) REVERT: Y 313 LYS cc_start: 0.8380 (mmmt) cc_final: 0.7580 (mttt) REVERT: Y 447 GLU cc_start: 0.8256 (tp30) cc_final: 0.7911 (tp30) REVERT: Y 684 THR cc_start: 0.7613 (OUTLIER) cc_final: 0.7230 (t) REVERT: Y 778 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8052 (tm-30) REVERT: Y 970 TRP cc_start: 0.8106 (t60) cc_final: 0.7665 (t60) outliers start: 10 outliers final: 7 residues processed: 90 average time/residue: 0.1060 time to fit residues: 13.6871 Evaluate side-chains 77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 368 VAL 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 677 ILE Chi-restraints excluded: chain Y residue 684 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: 3.9990 chunk 18 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 0.0050 chunk 21 optimal weight: 10.0000 overall best weight: 3.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.116132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.086119 restraints weight = 22832.987| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.34 r_work: 0.3227 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11107 Z= 0.257 Angle : 0.741 9.725 15856 Z= 0.391 Chirality : 0.042 0.221 1880 Planarity : 0.005 0.036 1379 Dihedral : 24.040 164.243 3413 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.96 % Favored : 84.78 % Rotamer: Outliers : 1.48 % Allowed : 21.71 % Favored : 76.81 % 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: -1.39 (0.31), residues: 782 helix: 1.40 (0.28), residues: 354 sheet: -2.39 (0.67), residues: 74 loop : -3.20 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 265 TYR 0.016 0.002 TYR Y 732 PHE 0.033 0.002 PHE Y 775 TRP 0.029 0.002 TRP Y 534 HIS 0.004 0.001 HIS Y 758 Details of bonding type rmsd covalent geometry : bond 0.00558 (11105) covalent geometry : angle 0.74064 (15851) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.40118 ( 2) hydrogen bonds : bond 0.05529 ( 441) hydrogen bonds : angle 3.96623 ( 1131) link_TRANS : bond 0.00079 ( 1) link_TRANS : angle 0.98504 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2538.79 seconds wall clock time: 44 minutes 7.59 seconds (2647.59 seconds total)