Starting phenix.real_space_refine on Fri Sep 11 16:31:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ny3_8980/09_2026/6ny3_8980.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ny3_8980/09_2026/6ny3_8980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ny3_8980/09_2026/6ny3_8980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ny3_8980/09_2026/6ny3_8980.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ny3_8980/09_2026/6ny3_8980.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ny3_8980/09_2026/6ny3_8980.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ny3_8980/09_2026/6ny3_8980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ny3_8980/09_2026/6ny3_8980.cif" } resolution = 3.7 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= 0.004 sd= 0.110 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 164 5.49 5 S 21 5.16 5 C 5880 2.51 5 N 1863 2.21 5 O 2286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 10214 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 614 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 485 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} 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: 1.90, per 1000 atoms: 0.19 Number of scatterers: 10214 At special positions: 0 Unit cell: (97.2, 139.5, 123.3, 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 164 15.00 O 2286 8.00 N 1863 7.00 C 5880 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=2.02 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: 0.79 Conformation dependent library (CDL) restraints added in 246.3 milliseconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 7 sheets defined 44.5% alpha, 7.7% beta 63 base pairs and 99 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'Y' and resid 4 through 13 removed outlier: 3.566A pdb=" N ILE Y 8 " --> pdb=" O ARG Y 4 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG Y 9 " --> pdb=" O ILE Y 5 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS Y 10 " --> pdb=" O ASN Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 42 Processing helix chain 'Y' and resid 60 through 88 removed outlier: 3.641A pdb=" N ASN Y 64 " --> pdb=" O ASN Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 90 through 98 Processing helix chain 'Y' and resid 222 through 260 removed outlier: 4.440A pdb=" N ASP Y 245 " --> pdb=" O SER Y 241 " (cutoff:3.500A) Processing helix chain 'Y' and resid 262 through 271 removed outlier: 4.476A pdb=" N ALA Y 268 " --> pdb=" O LEU Y 264 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 308 Processing helix chain 'Y' and resid 343 through 357 removed outlier: 3.953A pdb=" N LYS Y 357 " --> pdb=" O LEU Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 361 through 366 removed outlier: 3.917A pdb=" N TRP Y 365 " --> pdb=" O GLY Y 361 " (cutoff:3.500A) Processing helix chain 'Y' and resid 371 through 380 Processing helix chain 'Y' and resid 404 through 417 Processing helix chain 'Y' and resid 423 through 429 removed outlier: 4.306A pdb=" N ASP Y 427 " --> pdb=" O GLY Y 423 " (cutoff:3.500A) Processing helix chain 'Y' and resid 433 through 448 removed outlier: 3.575A pdb=" N LEU Y 440 " --> pdb=" O LYS Y 436 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS Y 443 " --> pdb=" O GLY Y 439 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU Y 445 " --> pdb=" O THR Y 441 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG Y 446 " --> pdb=" O SER Y 442 " (cutoff:3.500A) Processing helix chain 'Y' and resid 458 through 473 Processing helix chain 'Y' and resid 475 through 480 Processing helix chain 'Y' and resid 481 through 501 removed outlier: 4.371A pdb=" N TYR Y 485 " --> pdb=" O GLU Y 481 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA Y 486 " --> pdb=" O LYS Y 482 " (cutoff:3.500A) Processing helix chain 'Y' and resid 502 through 504 No H-bonds generated for 'chain 'Y' and resid 502 through 504' Processing helix chain 'Y' and resid 602 through 610 Processing helix chain 'Y' and resid 711 through 728 removed outlier: 3.884A pdb=" N ARG Y 728 " --> pdb=" O VAL Y 724 " (cutoff:3.500A) Processing helix chain 'Y' and resid 738 through 762 removed outlier: 3.904A pdb=" N ASN Y 742 " --> pdb=" O SER Y 738 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS Y 762 " --> pdb=" O HIS Y 758 " (cutoff:3.500A) Processing helix chain 'Y' and resid 783 through 787 Processing helix chain 'Y' and resid 790 through 802 removed outlier: 4.049A pdb=" N TYR Y 802 " --> pdb=" O ALA Y 798 " (cutoff:3.500A) Processing helix chain 'Y' and resid 886 through 892 Processing helix chain 'Y' and resid 897 through 904 Processing helix chain 'Y' and resid 906 through 914 removed outlier: 3.747A pdb=" N UNK Y 910 " --> pdb=" O UNK Y 906 " (cutoff:3.500A) Processing helix chain 'Y' and resid 945 through 950 Processing helix chain 'Y' and resid 965 through 978 removed outlier: 3.534A pdb=" N ARG Y 976 " --> pdb=" O ALA Y 972 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'Y' and resid 27 through 29 removed outlier: 3.605A pdb=" N ASN Y 626 " --> pdb=" O THR Y 651 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLU Y 653 " --> pdb=" O LEU Y 624 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU Y 624 " --> pdb=" O GLU Y 653 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG Y 510 " --> pdb=" O GLU Y 631 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 27 through 29 removed outlier: 3.605A pdb=" N ASN Y 626 " --> pdb=" O THR Y 651 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLU Y 653 " --> pdb=" O LEU Y 624 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU Y 624 " --> pdb=" O GLU Y 653 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Y' and resid 33 through 34 removed outlier: 3.695A pdb=" N ARG Y 33 " --> pdb=" O ALA Y 600 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 518 through 519 removed outlier: 4.031A pdb=" N SER Y 518 " --> pdb=" O GLN Y 527 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Y' and resid 557 through 558 removed outlier: 4.036A pdb=" N ARG Y 557 " --> pdb=" O THR Y 586 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Y' and resid 669 through 670 removed outlier: 6.363A pdb=" N ILE Y 669 " --> pdb=" O VAL Y 767 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA Y 769 " --> pdb=" O ILE Y 669 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU Y 766 " --> pdb=" O SER Y 812 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR Y 814 " --> pdb=" O LEU Y 766 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE Y 768 " --> pdb=" O THR Y 814 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 250 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 153 hydrogen bonds 288 hydrogen bond angles 0 basepair planarities 63 basepair parallelities 99 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1454 1.32 - 1.44: 3695 1.44 - 1.57: 5236 1.57 - 1.69: 323 1.69 - 1.81: 34 Bond restraints: 10742 Sorted by residual: bond pdb=" C3' DG C 12 " pdb=" O3' DG C 12 " ideal model delta sigma weight residual 1.435 1.382 0.053 1.30e-02 5.92e+03 1.64e+01 bond pdb=" N1 DC C 13 " pdb=" C6 DC C 13 " ideal model delta sigma weight residual 1.367 1.343 0.024 6.00e-03 2.78e+04 1.61e+01 bond pdb=" C4' DT C 9 " pdb=" C3' DT C 9 " ideal model delta sigma weight residual 1.529 1.491 0.038 1.00e-02 1.00e+04 1.46e+01 bond pdb=" C3' DT C 9 " pdb=" O3' DT C 9 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.44e+01 bond pdb=" C1' DT C 6 " pdb=" N1 DT C 6 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.40e+01 ... (remaining 10737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 14893 3.27 - 6.55: 363 6.55 - 9.82: 31 9.82 - 13.09: 4 13.09 - 16.37: 1 Bond angle restraints: 15292 Sorted by residual: angle pdb=" N GLY Y 572 " pdb=" CA GLY Y 572 " pdb=" C GLY Y 572 " ideal model delta sigma weight residual 113.18 129.55 -16.37 2.37e+00 1.78e-01 4.77e+01 angle pdb=" CA TRP Y 534 " pdb=" CB TRP Y 534 " pdb=" CG TRP Y 534 " ideal model delta sigma weight residual 113.60 125.99 -12.39 1.90e+00 2.77e-01 4.25e+01 angle pdb=" N SER Y 197 " pdb=" CA SER Y 197 " pdb=" C SER Y 197 " ideal model delta sigma weight residual 114.64 104.98 9.66 1.52e+00 4.33e-01 4.04e+01 angle pdb=" C3' G B 44 " pdb=" O3' G B 44 " pdb=" P U B 45 " ideal model delta sigma weight residual 119.70 126.24 -6.54 1.20e+00 6.94e-01 2.97e+01 angle pdb=" C ILE Y 198 " pdb=" N HIS Y 199 " pdb=" CA HIS Y 199 " ideal model delta sigma weight residual 121.54 131.42 -9.88 1.91e+00 2.74e-01 2.68e+01 ... (remaining 15287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 5497 34.22 - 68.44: 513 68.44 - 102.65: 28 102.65 - 136.87: 1 136.87 - 171.09: 3 Dihedral angle restraints: 6042 sinusoidal: 3385 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 -37.60 73.94 1 3.10e+00 1.04e-01 7.23e+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 36.34 -36.85 73.19 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' A B 10 " pdb=" C3' A B 10 " pdb=" C2' A B 10 " pdb=" C1' A B 10 " ideal model delta sinusoidal sigma weight residual 36.34 -35.93 72.28 1 3.10e+00 1.04e-01 6.95e+02 ... (remaining 6039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1366 0.070 - 0.140: 257 0.140 - 0.210: 88 0.210 - 0.280: 91 0.280 - 0.350: 14 Chirality restraints: 1816 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 -2.52 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CB ILE Y 677 " pdb=" CA ILE Y 677 " pdb=" CG1 ILE Y 677 " pdb=" CG2 ILE Y 677 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+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 -2.17 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 1813 not shown) Planarity restraints: 1364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP Y 534 " -0.025 2.00e-02 2.50e+03 1.97e-02 9.70e+00 pdb=" CG TRP Y 534 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP Y 534 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP Y 534 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP Y 534 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP Y 534 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP Y 534 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP Y 534 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP Y 534 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP Y 534 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 56 " -0.039 2.00e-02 2.50e+03 1.85e-02 9.41e+00 pdb=" N9 A B 56 " 0.045 2.00e-02 2.50e+03 pdb=" C8 A B 56 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 56 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 56 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A B 56 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A B 56 " -0.011 2.00e-02 2.50e+03 pdb=" N1 A B 56 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A B 56 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A B 56 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A B 56 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN Y 501 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO Y 502 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO Y 502 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO Y 502 " 0.040 5.00e-02 4.00e+02 ... (remaining 1361 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2340 2.78 - 3.31: 8487 3.31 - 3.84: 18053 3.84 - 4.37: 19591 4.37 - 4.90: 30769 Nonbonded interactions: 79240 Sorted by model distance: nonbonded pdb=" OH TYR Y 196 " pdb=" O SER Y 221 " model vdw 2.251 3.040 nonbonded pdb=" O4 U B 65 " pdb=" O6 G B 87 " model vdw 2.295 2.432 nonbonded pdb=" OG1 THR Y 603 " pdb=" OP2 A B 18 " model vdw 2.302 3.040 nonbonded pdb=" O SER Y 204 " pdb=" OG SER Y 204 " model vdw 2.321 3.040 nonbonded pdb=" O SER Y 661 " pdb=" OG SER Y 661 " model vdw 2.334 3.040 ... (remaining 79235 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 group one per residue 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.860 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 : 0.009 0.082 10744 Z= 0.528 Angle : 1.227 16.367 15297 Z= 0.704 Chirality : 0.085 0.350 1816 Planarity : 0.007 0.071 1363 Dihedral : 21.570 171.087 4312 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.64 % Allowed : 16.88 % Favored : 82.48 % Rotamer: Outliers : 0.33 % Allowed : 11.51 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -5.86 (0.20), residues: 782 helix: -3.34 (0.18), residues: 349 sheet: -4.27 (0.40), residues: 92 loop : -4.33 (0.24), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 787 TYR 0.022 0.003 TYR Y 732 PHE 0.039 0.004 PHE Y 609 TRP 0.053 0.003 TRP Y 534 HIS 0.019 0.004 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00941 / 0.53 (10742) covalent geometry : angle 1.22705 / 0.70 (15292) SS BOND : bond 0.00789 / 0.39 ( 1) SS BOND : angle 2.50922 / 1.58 ( 2) hydrogen bonds : bond 0.15717 / 17.23 ( 400) hydrogen bonds : angle 6.77320 / 8.13 ( 1020) link_TRANS : bond 0.00138 / 0.07 ( 1) link_TRANS : angle 0.78483 / 0.62 ( 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 88 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.304 Fit side-chains REVERT: Y 498 LEU cc_start: 0.8628 (mt) cc_final: 0.8302 (mt) REVERT: Y 950 ASN cc_start: 0.8438 (p0) cc_final: 0.8233 (p0) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.1351 time to fit residues: 15.7963 Evaluate side-chains 64 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.117579 restraints weight = 13368.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.119239 restraints weight = 9829.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.120228 restraints weight = 8048.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120961 restraints weight = 7111.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121294 restraints weight = 6588.718| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10744 Z= 0.194 Angle : 1.142 20.149 15297 Z= 0.501 Chirality : 0.091 1.269 1816 Planarity : 0.005 0.050 1363 Dihedral : 20.978 167.406 2872 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.83 % Favored : 84.91 % Rotamer: Outliers : 2.47 % Allowed : 16.12 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -4.14 (0.26), residues: 782 helix: -1.44 (0.26), residues: 343 sheet: -3.60 (0.49), residues: 85 loop : -3.92 (0.26), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Y 604 TYR 0.011 0.001 TYR Y 243 PHE 0.021 0.002 PHE Y 503 TRP 0.032 0.002 TRP Y 534 HIS 0.007 0.002 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.19 (10742) covalent geometry : angle 1.14160 / 0.50 (15292) SS BOND : bond 0.00111 / 0.06 ( 1) SS BOND : angle 1.38116 / 0.92 ( 2) hydrogen bonds : bond 0.06234 / 6.93 ( 400) hydrogen bonds : angle 4.71419 / 6.12 ( 1020) link_TRANS : bond 0.00058 / 0.03 ( 1) link_TRANS : angle 0.85158 / 0.79 ( 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 91 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: Y 639 ILE cc_start: 0.6541 (OUTLIER) cc_final: 0.6031 (pt) REVERT: Y 932 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8885 (m) outliers start: 15 outliers final: 6 residues processed: 88 average time/residue: 0.1153 time to fit residues: 13.9635 Evaluate side-chains 71 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 560 ASP Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 80 optimal weight: 0.0570 chunk 39 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.154456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120265 restraints weight = 13498.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121988 restraints weight = 9808.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.122905 restraints weight = 7979.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.123689 restraints weight = 7071.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124222 restraints weight = 6545.548| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10744 Z= 0.167 Angle : 0.927 13.433 15297 Z= 0.425 Chirality : 0.066 0.823 1816 Planarity : 0.004 0.049 1363 Dihedral : 20.766 172.251 2872 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.09 % Favored : 84.65 % Rotamer: Outliers : 3.45 % Allowed : 19.08 % Favored : 77.47 % 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: -3.39 (0.28), residues: 782 helix: -0.67 (0.28), residues: 337 sheet: -3.66 (0.50), residues: 85 loop : -3.52 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG Y 944 TYR 0.024 0.002 TYR Y 575 PHE 0.024 0.002 PHE Y 775 TRP 0.023 0.002 TRP Y 534 HIS 0.007 0.002 HIS Y 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (10742) covalent geometry : angle 0.92723 / 0.43 (15292) SS BOND : bond 0.00142 / 0.07 ( 1) SS BOND : angle 0.74465 / 0.50 ( 2) hydrogen bonds : bond 0.05796 / 6.40 ( 400) hydrogen bonds : angle 4.23099 / 5.49 ( 1020) link_TRANS : bond 0.00051 / 0.03 ( 1) link_TRANS : angle 0.91293 / 0.81 ( 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 90 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.352 Fit side-chains REVERT: Y 639 ILE cc_start: 0.6514 (OUTLIER) cc_final: 0.6068 (pt) outliers start: 21 outliers final: 10 residues processed: 86 average time/residue: 0.0940 time to fit residues: 12.0798 Evaluate side-chains 77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 782 THR Chi-restraints excluded: chain Y residue 924 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 39 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 0.0980 chunk 55 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 81 optimal weight: 0.0050 chunk 25 optimal weight: 0.9980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.157411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.123754 restraints weight = 13432.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.125415 restraints weight = 9700.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126659 restraints weight = 7844.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.127025 restraints weight = 6873.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127501 restraints weight = 6463.391| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10744 Z= 0.147 Angle : 0.883 14.392 15297 Z= 0.401 Chirality : 0.060 0.580 1816 Planarity : 0.004 0.047 1363 Dihedral : 20.510 172.932 2872 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.45 % Favored : 85.42 % Rotamer: Outliers : 3.45 % Allowed : 19.57 % 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: -2.95 (0.29), residues: 782 helix: -0.25 (0.28), residues: 343 sheet: -3.17 (0.54), residues: 89 loop : -3.47 (0.28), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 316 TYR 0.010 0.001 TYR Y 196 PHE 0.024 0.002 PHE Y 775 TRP 0.022 0.001 TRP Y 534 HIS 0.004 0.001 HIS Y 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (10742) covalent geometry : angle 0.88332 / 0.40 (15292) SS BOND : bond 0.00124 / 0.06 ( 1) SS BOND : angle 0.84582 / 0.57 ( 2) hydrogen bonds : bond 0.05206 / 5.81 ( 400) hydrogen bonds : angle 4.01434 / 5.20 ( 1020) link_TRANS : bond 0.00101 / 0.05 ( 1) link_TRANS : angle 0.90067 / 0.81 ( 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 94 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.223 Fit side-chains REVERT: Y 639 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.6150 (pt) REVERT: Y 920 GLN cc_start: 0.6797 (tp-100) cc_final: 0.6578 (tp40) REVERT: Y 960 LYS cc_start: 0.8568 (tppt) cc_final: 0.8094 (tptt) outliers start: 21 outliers final: 11 residues processed: 87 average time/residue: 0.0881 time to fit residues: 11.5968 Evaluate side-chains 73 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 524 HIS Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 40.0000 chunk 18 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.152867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.120122 restraints weight = 13508.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.120132 restraints weight = 15124.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122889 restraints weight = 13182.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.123043 restraints weight = 8955.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.123053 restraints weight = 7864.716| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10744 Z= 0.211 Angle : 0.915 10.540 15297 Z= 0.418 Chirality : 0.060 0.580 1816 Planarity : 0.004 0.043 1363 Dihedral : 20.395 174.598 2872 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.47 % Favored : 84.27 % Rotamer: Outliers : 3.29 % Allowed : 21.05 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.72 (0.30), residues: 782 helix: -0.14 (0.28), residues: 345 sheet: -2.91 (0.57), residues: 85 loop : -3.32 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 654 TYR 0.020 0.002 TYR Y 575 PHE 0.023 0.002 PHE Y 775 TRP 0.025 0.002 TRP Y 534 HIS 0.005 0.001 HIS Y 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (10742) covalent geometry : angle 0.91506 / 0.42 (15292) SS BOND : bond 0.00141 / 0.07 ( 1) SS BOND : angle 0.70369 / 0.47 ( 2) hydrogen bonds : bond 0.05793 / 6.49 ( 400) hydrogen bonds : angle 3.91889 / 5.03 ( 1020) link_TRANS : bond 0.00158 / 0.08 ( 1) link_TRANS : angle 0.73573 / 0.62 ( 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 82 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.293 Fit side-chains REVERT: Y 434 ASP cc_start: 0.8262 (t0) cc_final: 0.8055 (t0) REVERT: Y 639 ILE cc_start: 0.6623 (OUTLIER) cc_final: 0.6185 (pt) REVERT: Y 920 GLN cc_start: 0.6751 (tp-100) cc_final: 0.6509 (tp40) outliers start: 20 outliers final: 16 residues processed: 77 average time/residue: 0.0833 time to fit residues: 9.6061 Evaluate side-chains 73 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 254 VAL Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 418 TYR Chi-restraints excluded: chain Y residue 524 HIS Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 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 952 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 17 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3745 r_free = 0.3745 target = 0.154764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.121419 restraints weight = 13556.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.121794 restraints weight = 10565.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.122427 restraints weight = 9307.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.122858 restraints weight = 8070.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123187 restraints weight = 7487.224| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10744 Z= 0.163 Angle : 0.875 11.628 15297 Z= 0.399 Chirality : 0.057 0.464 1816 Planarity : 0.004 0.045 1363 Dihedral : 20.301 176.004 2872 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.83 % Favored : 85.04 % Rotamer: Outliers : 3.29 % Allowed : 22.20 % Favored : 74.51 % 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: -2.39 (0.30), residues: 782 helix: 0.30 (0.29), residues: 337 sheet: -2.82 (0.58), residues: 84 loop : -3.25 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 316 TYR 0.013 0.001 TYR Y 575 PHE 0.030 0.002 PHE Y 775 TRP 0.025 0.001 TRP Y 534 HIS 0.004 0.001 HIS Y 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (10742) covalent geometry : angle 0.87472 / 0.40 (15292) SS BOND : bond 0.00103 / 0.05 ( 1) SS BOND : angle 0.64322 / 0.40 ( 2) hydrogen bonds : bond 0.05442 / 6.14 ( 400) hydrogen bonds : angle 3.85011 / 4.96 ( 1020) link_TRANS : bond 0.00152 / 0.08 ( 1) link_TRANS : angle 0.75382 / 0.63 ( 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 83 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.300 Fit side-chains REVERT: Y 434 ASP cc_start: 0.8220 (t0) cc_final: 0.8015 (t0) REVERT: Y 639 ILE cc_start: 0.6543 (OUTLIER) cc_final: 0.6112 (pt) REVERT: Y 920 GLN cc_start: 0.6867 (tp-100) cc_final: 0.6654 (tp40) outliers start: 20 outliers final: 15 residues processed: 77 average time/residue: 0.0828 time to fit residues: 10.0242 Evaluate side-chains 77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 418 TYR Chi-restraints excluded: chain Y residue 515 SER Chi-restraints excluded: chain Y residue 524 HIS Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 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 952 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 66 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 19 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.152630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.119239 restraints weight = 13490.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120077 restraints weight = 10521.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.120552 restraints weight = 8698.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.121008 restraints weight = 7824.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.121213 restraints weight = 7470.545| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10744 Z= 0.170 Angle : 0.876 12.262 15297 Z= 0.398 Chirality : 0.057 0.468 1816 Planarity : 0.004 0.044 1363 Dihedral : 20.241 177.171 2872 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.09 % Favored : 84.78 % Rotamer: Outliers : 3.12 % Allowed : 23.52 % Favored : 73.36 % 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: -2.37 (0.30), residues: 782 helix: 0.35 (0.29), residues: 343 sheet: -2.97 (0.56), residues: 91 loop : -3.26 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 316 TYR 0.024 0.001 TYR Y 575 PHE 0.026 0.002 PHE Y 775 TRP 0.023 0.001 TRP Y 534 HIS 0.005 0.001 HIS Y 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (10742) covalent geometry : angle 0.87476 / 0.40 (15292) SS BOND : bond 0.00677 / 0.34 ( 1) SS BOND : angle 3.37184 / 5.51 ( 2) hydrogen bonds : bond 0.05541 / 6.24 ( 400) hydrogen bonds : angle 3.78870 / 4.86 ( 1020) link_TRANS : bond 0.00124 / 0.06 ( 1) link_TRANS : angle 0.70565 / 0.59 ( 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: 19 poor density : 63 time to evaluate : 0.327 Fit side-chains REVERT: Y 639 ILE cc_start: 0.6602 (OUTLIER) cc_final: 0.6172 (pt) REVERT: Y 775 PHE cc_start: 0.7383 (t80) cc_final: 0.7155 (t80) outliers start: 19 outliers final: 16 residues processed: 76 average time/residue: 0.0821 time to fit residues: 9.7911 Evaluate side-chains 78 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 36 THR Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 285 HIS Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 418 TYR Chi-restraints excluded: chain Y residue 524 HIS Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 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 952 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 0.0770 chunk 63 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.156371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118742 restraints weight = 13901.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121645 restraints weight = 8319.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123556 restraints weight = 6029.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124552 restraints weight = 4948.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125362 restraints weight = 4432.641| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10744 Z= 0.143 Angle : 0.840 13.606 15297 Z= 0.381 Chirality : 0.055 0.404 1816 Planarity : 0.004 0.046 1363 Dihedral : 20.176 178.917 2872 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.07 % Favored : 85.81 % Rotamer: Outliers : 3.12 % Allowed : 23.36 % Favored : 73.52 % 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: 0.52 (0.29), residues: 344 sheet: -3.07 (0.57), residues: 81 loop : -3.17 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 529 TYR 0.016 0.001 TYR Y 575 PHE 0.018 0.001 PHE Y 775 TRP 0.022 0.001 TRP Y 534 HIS 0.002 0.001 HIS Y 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (10742) covalent geometry : angle 0.83945 / 0.38 (15292) SS BOND : bond 0.00304 / 0.15 ( 1) SS BOND : angle 2.95353 / 3.03 ( 2) hydrogen bonds : bond 0.05131 / 5.79 ( 400) hydrogen bonds : angle 3.72621 / 4.79 ( 1020) link_TRANS : bond 0.00139 / 0.07 ( 1) link_TRANS : angle 0.84481 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.357 Fit side-chains REVERT: Y 286 THR cc_start: 0.8659 (p) cc_final: 0.8396 (t) REVERT: Y 639 ILE cc_start: 0.6077 (OUTLIER) cc_final: 0.5748 (pt) REVERT: Y 775 PHE cc_start: 0.7549 (t80) cc_final: 0.7247 (t80) outliers start: 19 outliers final: 15 residues processed: 76 average time/residue: 0.0885 time to fit residues: 10.3370 Evaluate side-chains 76 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 57 ILE Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 285 HIS Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 441 THR Chi-restraints excluded: chain Y residue 524 HIS Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 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 952 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 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 = 0.3792 r_free = 0.3792 target = 0.154921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116373 restraints weight = 13866.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119589 restraints weight = 7803.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121509 restraints weight = 5464.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.122917 restraints weight = 4427.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123624 restraints weight = 3887.215| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10744 Z= 0.156 Angle : 0.846 13.374 15297 Z= 0.385 Chirality : 0.055 0.417 1816 Planarity : 0.004 0.044 1363 Dihedral : 20.120 179.642 2872 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.83 % Favored : 85.04 % Rotamer: Outliers : 2.96 % Allowed : 24.51 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.11 (0.30), residues: 782 helix: 0.69 (0.29), residues: 337 sheet: -3.13 (0.57), residues: 76 loop : -3.17 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 787 TYR 0.018 0.001 TYR Y 575 PHE 0.016 0.002 PHE Y 775 TRP 0.020 0.001 TRP Y 534 HIS 0.004 0.001 HIS Y 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (10742) covalent geometry : angle 0.84545 / 0.38 (15292) SS BOND : bond 0.00193 / 0.10 ( 1) SS BOND : angle 1.69391 / 1.28 ( 2) hydrogen bonds : bond 0.05246 / 5.90 ( 400) hydrogen bonds : angle 3.67939 / 4.70 ( 1020) link_TRANS : bond 0.00110 / 0.05 ( 1) link_TRANS : angle 0.79494 / 0.67 ( 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 78 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.307 Fit side-chains REVERT: Y 639 ILE cc_start: 0.6063 (OUTLIER) cc_final: 0.5740 (pt) outliers start: 18 outliers final: 14 residues processed: 70 average time/residue: 0.0798 time to fit residues: 8.7374 Evaluate side-chains 75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 57 ILE Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 285 HIS Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 524 HIS Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 782 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 20 optimal weight: 0.4980 chunk 4 optimal weight: 40.0000 chunk 76 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.157156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119699 restraints weight = 13873.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122544 restraints weight = 8301.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124405 restraints weight = 6030.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125620 restraints weight = 4939.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.126252 restraints weight = 4394.641| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10744 Z= 0.142 Angle : 0.831 14.125 15297 Z= 0.379 Chirality : 0.054 0.386 1816 Planarity : 0.004 0.045 1363 Dihedral : 20.094 179.428 2872 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.19 % Favored : 85.68 % Rotamer: Outliers : 2.47 % Allowed : 24.84 % Favored : 72.70 % 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: -2.02 (0.30), residues: 782 helix: 0.81 (0.30), residues: 338 sheet: -3.06 (0.57), residues: 81 loop : -3.17 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 604 TYR 0.014 0.001 TYR Y 575 PHE 0.036 0.002 PHE Y 775 TRP 0.022 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (10742) covalent geometry : angle 0.83044 / 0.38 (15292) SS BOND : bond 0.00133 / 0.07 ( 1) SS BOND : angle 1.74399 / 1.15 ( 2) hydrogen bonds : bond 0.05014 / 5.65 ( 400) hydrogen bonds : angle 3.66793 / 4.69 ( 1020) link_TRANS : bond 0.00121 / 0.06 ( 1) link_TRANS : angle 0.90146 / 0.77 ( 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 79 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.276 Fit side-chains REVERT: Y 639 ILE cc_start: 0.6160 (OUTLIER) cc_final: 0.5848 (pt) outliers start: 15 outliers final: 14 residues processed: 72 average time/residue: 0.0884 time to fit residues: 9.7368 Evaluate side-chains 75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 285 HIS Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 524 HIS Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 634 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 669 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 6.9990 chunk 51 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.153576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114777 restraints weight = 13937.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117892 restraints weight = 7894.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119967 restraints weight = 5567.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121227 restraints weight = 4494.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.121915 restraints weight = 3952.513| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10744 Z= 0.203 Angle : 0.879 12.836 15297 Z= 0.401 Chirality : 0.056 0.422 1816 Planarity : 0.004 0.043 1363 Dihedral : 20.103 179.256 2872 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.22 % Favored : 84.65 % Rotamer: Outliers : 2.80 % Allowed : 25.16 % Favored : 72.04 % 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: -2.15 (0.30), residues: 782 helix: 0.66 (0.29), residues: 343 sheet: -3.11 (0.58), residues: 76 loop : -3.25 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 604 TYR 0.025 0.002 TYR Y 575 PHE 0.042 0.002 PHE Y 775 TRP 0.025 0.001 TRP Y 534 HIS 0.006 0.001 HIS Y 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (10742) covalent geometry : angle 0.87904 / 0.40 (15292) SS BOND : bond 0.00317 / 0.16 ( 1) SS BOND : angle 1.59561 / 1.02 ( 2) hydrogen bonds : bond 0.05636 / 6.35 ( 400) hydrogen bonds : angle 3.69361 / 4.69 ( 1020) link_TRANS : bond 0.00148 / 0.07 ( 1) link_TRANS : angle 0.83891 / 0.70 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1611.61 seconds wall clock time: 28 minutes 38.56 seconds (1718.56 seconds total)