Starting phenix.real_space_refine on Mon Jul 28 21:14:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ny2_8996/07_2025/6ny2_8996.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ny2_8996/07_2025/6ny2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ny2_8996/07_2025/6ny2_8996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ny2_8996/07_2025/6ny2_8996.map" model { file = "/net/cci-nas-00/data/ceres_data/6ny2_8996/07_2025/6ny2_8996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ny2_8996/07_2025/6ny2_8996.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 4, 'TYR:plan': 1, 'UNK:plan-1': 57, 'ASP:plan': 15, 'GLU:plan': 23, 'ARG:plan': 3} 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: {'GLU:plan': 3, 'UNK:plan-1': 64, '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: 8.17, per 1000 atoms: 0.78 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: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 4.77 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: 5.66 Time building geometry restraints manager: 3.24 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 87.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.430 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 35.340 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.210 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.035 0.002 TRP Y 534 HIS 0.015 0.002 HIS Y 250 PHE 0.042 0.003 PHE Y 609 TYR 0.018 0.003 TYR Y 818 ARG 0.009 0.001 ARG Y 673 Details of bonding type rmsd link_TRANS : bond 0.00044 ( 1) link_TRANS : angle 0.93798 ( 3) hydrogen bonds : bond 0.13859 ( 441) hydrogen bonds : angle 6.64515 ( 1131) SS BOND : bond 0.00116 ( 1) SS BOND : angle 1.71962 ( 2) covalent geometry : bond 0.00704 (11105) covalent geometry : angle 1.01526 (15851) *********************** 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 : 0.965 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: 0.5881 time to fit residues: 66.2053 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 : 0.998 ------------------------------------------------------------------------------- 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 79 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.118441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.088986 restraints weight = 22279.561| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.29 r_work: 0.3276 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1486 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= 0.150 Angle : 0.697 10.244 15856 Z= 0.370 Chirality : 0.039 0.224 1880 Planarity : 0.005 0.041 1379 Dihedral : 24.357 174.735 3415 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.32 % Favored : 85.55 % Rotamer: Outliers : 2.47 % Allowed : 12.83 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.28), residues: 782 helix: -0.18 (0.26), residues: 353 sheet: -2.16 (0.62), residues: 78 loop : -3.93 (0.26), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP Y 534 HIS 0.005 0.001 HIS Y 250 PHE 0.026 0.002 PHE Y 503 TYR 0.012 0.001 TYR Y 711 ARG 0.005 0.000 ARG Y 777 Details of bonding type rmsd link_TRANS : bond 0.00004 ( 1) link_TRANS : angle 0.55808 ( 3) hydrogen bonds : bond 0.05382 ( 441) hydrogen bonds : angle 4.29947 ( 1131) SS BOND : bond 0.00064 ( 1) SS BOND : angle 0.92939 ( 2) covalent geometry : bond 0.00303 (11105) covalent geometry : angle 0.69729 (15851) *********************** 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 : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 86 GLU cc_start: 0.8632 (tp30) cc_final: 0.8390 (tp30) REVERT: Y 778 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8274 (tm-30) REVERT: Y 784 MET cc_start: 0.8873 (mmm) cc_final: 0.8199 (mmm) REVERT: Y 812 SER cc_start: 0.8703 (t) cc_final: 0.8406 (p) REVERT: Y 956 PHE cc_start: 0.7362 (t80) cc_final: 0.7106 (t80) REVERT: Y 970 TRP cc_start: 0.8198 (t60) cc_final: 0.7621 (t60) outliers start: 15 outliers final: 9 residues processed: 88 average time/residue: 0.3529 time to fit residues: 43.9251 Evaluate side-chains 70 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 199 HIS 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 73 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.112506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.082375 restraints weight = 22833.328| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.32 r_work: 0.3156 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 11107 Z= 0.337 Angle : 0.816 11.590 15856 Z= 0.432 Chirality : 0.045 0.226 1880 Planarity : 0.005 0.041 1379 Dihedral : 24.428 167.980 3413 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 16.88 % Favored : 82.86 % Rotamer: Outliers : 3.95 % Allowed : 17.11 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.29), residues: 782 helix: 0.27 (0.28), residues: 360 sheet: -2.54 (0.59), residues: 82 loop : -3.93 (0.26), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP Y 534 HIS 0.007 0.002 HIS Y 250 PHE 0.032 0.003 PHE Y 609 TYR 0.014 0.002 TYR Y 243 ARG 0.005 0.001 ARG Y 604 Details of bonding type rmsd link_TRANS : bond 0.00171 ( 1) link_TRANS : angle 1.10639 ( 3) hydrogen bonds : bond 0.06387 ( 441) hydrogen bonds : angle 4.36200 ( 1131) SS BOND : bond 0.00112 ( 1) SS BOND : angle 1.01594 ( 2) covalent geometry : bond 0.00731 (11105) covalent geometry : angle 0.81599 (15851) *********************** 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 80 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.879 Fit side-chains REVERT: Y 736 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.6803 (p90) REVERT: Y 778 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8275 (tm-30) REVERT: Y 784 MET cc_start: 0.8902 (mmm) cc_final: 0.7913 (mmm) REVERT: Y 956 PHE cc_start: 0.7504 (t80) cc_final: 0.7272 (t80) REVERT: Y 970 TRP cc_start: 0.8302 (t60) cc_final: 0.7519 (t60) outliers start: 24 outliers final: 17 residues processed: 74 average time/residue: 0.2319 time to fit residues: 25.0318 Evaluate side-chains 67 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 67 MET Chi-restraints excluded: chain Y residue 91 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 302 MET Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 425 VAL Chi-restraints excluded: chain Y residue 531 LEU Chi-restraints excluded: chain Y residue 583 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 736 PHE Chi-restraints excluded: chain Y residue 765 VAL Chi-restraints excluded: chain Y residue 807 SER 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 58 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 90 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.115059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084920 restraints weight = 22688.329| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.32 r_work: 0.3207 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11107 Z= 0.207 Angle : 0.711 10.281 15856 Z= 0.381 Chirality : 0.040 0.221 1880 Planarity : 0.004 0.037 1379 Dihedral : 24.368 170.224 3413 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.22 % Favored : 84.65 % Rotamer: Outliers : 3.95 % Allowed : 18.75 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.30), residues: 782 helix: 0.63 (0.28), residues: 361 sheet: -2.57 (0.59), residues: 83 loop : -3.70 (0.27), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Y 534 HIS 0.016 0.002 HIS Y 91 PHE 0.018 0.002 PHE Y 609 TYR 0.013 0.002 TYR Y 818 ARG 0.003 0.000 ARG Y 753 Details of bonding type rmsd link_TRANS : bond 0.00084 ( 1) link_TRANS : angle 0.97903 ( 3) hydrogen bonds : bond 0.05537 ( 441) hydrogen bonds : angle 4.16341 ( 1131) SS BOND : bond 0.00048 ( 1) SS BOND : angle 0.89547 ( 2) covalent geometry : bond 0.00440 (11105) covalent geometry : angle 0.71131 (15851) *********************** 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 80 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.928 Fit side-chains REVERT: Y 100 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8580 (tt0) REVERT: Y 736 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7149 (p90) REVERT: Y 778 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8259 (tm-30) REVERT: Y 784 MET cc_start: 0.8853 (mmm) cc_final: 0.7959 (mmm) REVERT: Y 956 PHE cc_start: 0.7399 (t80) cc_final: 0.7169 (t80) REVERT: Y 970 TRP cc_start: 0.8232 (t60) cc_final: 0.7480 (t60) outliers start: 24 outliers final: 15 residues processed: 77 average time/residue: 0.3018 time to fit residues: 35.7419 Evaluate side-chains 69 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 67 MET Chi-restraints excluded: chain Y residue 100 GLN Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 583 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 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 Chi-restraints excluded: chain Y residue 967 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 41 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 57 optimal weight: 0.0270 chunk 79 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.119758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.090494 restraints weight = 22463.270| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.32 r_work: 0.3313 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11107 Z= 0.133 Angle : 0.645 8.389 15856 Z= 0.345 Chirality : 0.038 0.228 1880 Planarity : 0.004 0.034 1379 Dihedral : 24.176 179.798 3413 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.47 % Favored : 84.53 % Rotamer: Outliers : 3.12 % Allowed : 19.08 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.31), residues: 782 helix: 1.08 (0.29), residues: 361 sheet: -2.13 (0.62), residues: 78 loop : -3.51 (0.28), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 443 PHE 0.015 0.001 PHE Y 503 TYR 0.015 0.001 TYR Y 711 ARG 0.002 0.000 ARG Y 741 Details of bonding type rmsd link_TRANS : bond 0.00027 ( 1) link_TRANS : angle 1.10125 ( 3) hydrogen bonds : bond 0.04761 ( 441) hydrogen bonds : angle 3.88790 ( 1131) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.82982 ( 2) covalent geometry : bond 0.00271 (11105) covalent geometry : angle 0.64452 (15851) *********************** 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 98 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.826 Fit side-chains REVERT: Y 86 GLU cc_start: 0.8647 (tp30) cc_final: 0.8223 (tm-30) REVERT: Y 265 ARG cc_start: 0.8570 (tmm-80) cc_final: 0.8207 (tmm-80) REVERT: Y 766 LEU cc_start: 0.9095 (mt) cc_final: 0.8813 (mt) REVERT: Y 778 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8170 (tm-30) REVERT: Y 784 MET cc_start: 0.8803 (mmm) cc_final: 0.8114 (mmm) REVERT: Y 812 SER cc_start: 0.8652 (t) cc_final: 0.8401 (p) REVERT: Y 970 TRP cc_start: 0.8184 (t60) cc_final: 0.7722 (t60) outliers start: 19 outliers final: 7 residues processed: 93 average time/residue: 0.2313 time to fit residues: 31.5146 Evaluate side-chains 73 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 765 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 11 optimal weight: 0.0970 chunk 71 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.3980 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.118218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088694 restraints weight = 22572.717| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.33 r_work: 0.3283 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2488 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= 0.154 Angle : 0.646 8.017 15856 Z= 0.345 Chirality : 0.038 0.217 1880 Planarity : 0.004 0.044 1379 Dihedral : 24.127 173.893 3413 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.60 % Favored : 84.40 % Rotamer: Outliers : 2.80 % Allowed : 20.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.31), residues: 782 helix: 1.27 (0.29), residues: 356 sheet: -2.17 (0.62), residues: 78 loop : -3.40 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 758 PHE 0.015 0.002 PHE Y 775 TYR 0.011 0.001 TYR Y 818 ARG 0.002 0.000 ARG Y 734 Details of bonding type rmsd link_TRANS : bond 0.00032 ( 1) link_TRANS : angle 1.20612 ( 3) hydrogen bonds : bond 0.04747 ( 441) hydrogen bonds : angle 3.84437 ( 1131) SS BOND : bond 0.00020 ( 1) SS BOND : angle 0.65325 ( 2) covalent geometry : bond 0.00323 (11105) covalent geometry : angle 0.64597 (15851) *********************** 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: 17 poor density : 66 time to evaluate : 0.820 Fit side-chains REVERT: Y 31 LEU cc_start: 0.8319 (tp) cc_final: 0.8007 (tp) REVERT: Y 265 ARG cc_start: 0.8588 (tmm-80) cc_final: 0.8241 (tmm-80) REVERT: Y 778 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8188 (tm-30) REVERT: Y 784 MET cc_start: 0.8804 (mmm) cc_final: 0.8108 (mmm) REVERT: Y 970 TRP cc_start: 0.8166 (t60) cc_final: 0.7601 (t60) outliers start: 17 outliers final: 12 residues processed: 79 average time/residue: 0.2067 time to fit residues: 24.4520 Evaluate side-chains 75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 425 VAL Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 765 VAL 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 64 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 92 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.118599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.089161 restraints weight = 22820.688| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.33 r_work: 0.3289 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11107 Z= 0.149 Angle : 0.645 7.955 15856 Z= 0.343 Chirality : 0.037 0.218 1880 Planarity : 0.004 0.043 1379 Dihedral : 24.043 174.850 3413 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.98 % Favored : 84.02 % Rotamer: Outliers : 2.63 % Allowed : 20.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.31), residues: 782 helix: 1.36 (0.29), residues: 356 sheet: -2.24 (0.63), residues: 76 loop : -3.28 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 443 PHE 0.028 0.002 PHE Y 775 TYR 0.011 0.001 TYR Y 818 ARG 0.003 0.000 ARG Y 777 Details of bonding type rmsd link_TRANS : bond 0.00007 ( 1) link_TRANS : angle 1.10743 ( 3) hydrogen bonds : bond 0.04704 ( 441) hydrogen bonds : angle 3.79043 ( 1131) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.66077 ( 2) covalent geometry : bond 0.00312 (11105) covalent geometry : angle 0.64457 (15851) *********************** 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 88 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.875 Fit side-chains REVERT: Y 31 LEU cc_start: 0.8217 (tp) cc_final: 0.7886 (tp) REVERT: Y 47 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7313 (mtp180) REVERT: Y 265 ARG cc_start: 0.8579 (tmm-80) cc_final: 0.8313 (tmm-80) REVERT: Y 778 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8243 (tm-30) REVERT: Y 784 MET cc_start: 0.8791 (mmm) cc_final: 0.8117 (mmm) REVERT: Y 970 TRP cc_start: 0.8178 (t60) cc_final: 0.7595 (t60) outliers start: 16 outliers final: 14 residues processed: 85 average time/residue: 0.2167 time to fit residues: 27.1517 Evaluate side-chains 78 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 30 LEU Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 425 VAL Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 630 ILE 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 765 VAL Chi-restraints excluded: chain Y residue 807 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 11 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 23 optimal weight: 0.0000 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.116114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.086473 restraints weight = 22623.394| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.31 r_work: 0.3235 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11107 Z= 0.204 Angle : 0.686 9.218 15856 Z= 0.365 Chirality : 0.039 0.222 1880 Planarity : 0.004 0.041 1379 Dihedral : 24.061 169.922 3413 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.47 % Favored : 84.40 % Rotamer: Outliers : 3.62 % Allowed : 21.55 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.31), residues: 782 helix: 1.31 (0.29), residues: 356 sheet: -2.50 (0.61), residues: 83 loop : -3.30 (0.28), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 758 PHE 0.034 0.002 PHE Y 775 TYR 0.013 0.002 TYR Y 575 ARG 0.003 0.000 ARG Y 753 Details of bonding type rmsd link_TRANS : bond 0.00053 ( 1) link_TRANS : angle 1.09847 ( 3) hydrogen bonds : bond 0.05132 ( 441) hydrogen bonds : angle 3.88874 ( 1131) SS BOND : bond 0.00025 ( 1) SS BOND : angle 0.51564 ( 2) covalent geometry : bond 0.00437 (11105) covalent geometry : angle 0.68627 (15851) *********************** 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 81 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.898 Fit side-chains REVERT: Y 55 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7616 (mm-40) REVERT: Y 265 ARG cc_start: 0.8616 (tmm-80) cc_final: 0.8328 (tmm-80) REVERT: Y 736 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7971 (p90) REVERT: Y 778 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8197 (tm-30) REVERT: Y 784 MET cc_start: 0.8810 (mmm) cc_final: 0.8135 (mmm) REVERT: Y 970 TRP cc_start: 0.8243 (t60) cc_final: 0.7544 (t60) outliers start: 22 outliers final: 17 residues processed: 75 average time/residue: 0.2249 time to fit residues: 24.8502 Evaluate side-chains 75 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 55 GLN 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 341 VAL Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 574 LEU Chi-restraints excluded: chain Y residue 615 LEU Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 736 PHE Chi-restraints excluded: chain Y residue 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 47 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.116852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.087260 restraints weight = 22835.633| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.33 r_work: 0.3250 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11107 Z= 0.179 Angle : 0.673 8.711 15856 Z= 0.358 Chirality : 0.039 0.221 1880 Planarity : 0.004 0.043 1379 Dihedral : 24.017 172.743 3413 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.60 % Favored : 84.27 % Rotamer: Outliers : 3.62 % Allowed : 21.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.31), residues: 782 helix: 1.33 (0.29), residues: 356 sheet: -2.52 (0.63), residues: 80 loop : -3.24 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 758 PHE 0.036 0.002 PHE Y 775 TYR 0.014 0.001 TYR Y 575 ARG 0.002 0.000 ARG Y 753 Details of bonding type rmsd link_TRANS : bond 0.00040 ( 1) link_TRANS : angle 1.12644 ( 3) hydrogen bonds : bond 0.04987 ( 441) hydrogen bonds : angle 3.87215 ( 1131) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.57917 ( 2) covalent geometry : bond 0.00381 (11105) covalent geometry : angle 0.67247 (15851) *********************** 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 84 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.830 Fit side-chains REVERT: Y 265 ARG cc_start: 0.8610 (tmm-80) cc_final: 0.8312 (tmm-80) REVERT: Y 736 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.7968 (p90) REVERT: Y 778 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8237 (tm-30) REVERT: Y 784 MET cc_start: 0.8814 (mmm) cc_final: 0.8142 (mmm) REVERT: Y 970 TRP cc_start: 0.8213 (t60) cc_final: 0.7537 (t60) outliers start: 22 outliers final: 16 residues processed: 79 average time/residue: 0.2209 time to fit residues: 26.0888 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 : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 302 MET Chi-restraints excluded: chain Y residue 341 VAL Chi-restraints excluded: chain Y residue 425 VAL Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 615 LEU Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 736 PHE Chi-restraints excluded: chain Y residue 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 56 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.112492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.082414 restraints weight = 22841.108| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.33 r_work: 0.3156 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11107 Z= 0.342 Angle : 0.811 11.013 15856 Z= 0.427 Chirality : 0.045 0.226 1880 Planarity : 0.005 0.044 1379 Dihedral : 24.215 164.564 3413 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.39 % Favored : 82.48 % Rotamer: Outliers : 3.62 % Allowed : 22.04 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.30), residues: 782 helix: 0.88 (0.28), residues: 364 sheet: -2.22 (0.62), residues: 79 loop : -3.68 (0.27), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP Y 534 HIS 0.005 0.002 HIS Y 758 PHE 0.040 0.003 PHE Y 775 TYR 0.022 0.002 TYR Y 575 ARG 0.005 0.001 ARG Y 604 Details of bonding type rmsd link_TRANS : bond 0.00193 ( 1) link_TRANS : angle 1.20704 ( 3) hydrogen bonds : bond 0.06268 ( 441) hydrogen bonds : angle 4.23527 ( 1131) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.57240 ( 2) covalent geometry : bond 0.00740 (11105) covalent geometry : angle 0.81043 (15851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: Y 265 ARG cc_start: 0.8607 (tmm-80) cc_final: 0.8213 (tmm-80) REVERT: Y 736 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.7443 (p90) REVERT: Y 778 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8282 (tm-30) REVERT: Y 784 MET cc_start: 0.8877 (mmm) cc_final: 0.8031 (mmm) REVERT: Y 970 TRP cc_start: 0.8287 (t60) cc_final: 0.7442 (t60) outliers start: 22 outliers final: 17 residues processed: 72 average time/residue: 0.2097 time to fit residues: 22.7350 Evaluate side-chains 70 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 341 VAL 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 531 LEU Chi-restraints excluded: chain Y residue 615 LEU Chi-restraints excluded: chain Y residue 630 ILE Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 736 PHE Chi-restraints excluded: chain Y residue 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 89 optimal weight: 20.0000 chunk 81 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.117762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.088035 restraints weight = 22679.721| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.32 r_work: 0.3263 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11107 Z= 0.151 Angle : 0.675 8.600 15856 Z= 0.359 Chirality : 0.038 0.219 1880 Planarity : 0.004 0.046 1379 Dihedral : 24.043 175.625 3413 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.22 % Favored : 84.65 % Rotamer: Outliers : 2.96 % Allowed : 22.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.31), residues: 782 helix: 1.26 (0.29), residues: 361 sheet: -2.83 (0.57), residues: 89 loop : -3.40 (0.29), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Y 534 HIS 0.003 0.001 HIS Y 524 PHE 0.025 0.002 PHE Y 775 TYR 0.012 0.001 TYR Y 575 ARG 0.003 0.000 ARG Y 753 Details of bonding type rmsd link_TRANS : bond 0.00008 ( 1) link_TRANS : angle 1.16487 ( 3) hydrogen bonds : bond 0.04982 ( 441) hydrogen bonds : angle 3.90747 ( 1131) SS BOND : bond 0.00080 ( 1) SS BOND : angle 0.90736 ( 2) covalent geometry : bond 0.00316 (11105) covalent geometry : angle 0.67532 (15851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6578.99 seconds wall clock time: 119 minutes 14.92 seconds (7154.92 seconds total)