Starting phenix.real_space_refine on Fri Feb 14 22:20:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ny2_8996/02_2025/6ny2_8996.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ny2_8996/02_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_8996/02_2025/6ny2_8996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ny2_8996/02_2025/6ny2_8996.map" model { file = "/net/cci-nas-00/data/ceres_data/6ny2_8996/02_2025/6ny2_8996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ny2_8996/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.52, per 1000 atoms: 0.62 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 1.0 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: 4.56 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: 5.52 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1893 1.33 - 1.45: 3610 1.45 - 1.57: 5213 1.57 - 1.69: 355 1.69 - 1.82: 34 Bond restraints: 11105 Sorted by residual: bond pdb=" C ASN Y 501 " pdb=" N PRO Y 502 " ideal model delta sigma weight residual 1.334 1.355 -0.021 8.40e-03 1.42e+04 6.32e+00 bond pdb=" CA LEU Y 615 " pdb=" CB LEU Y 615 " ideal model delta sigma weight residual 1.531 1.457 0.073 3.28e-02 9.30e+02 5.00e+00 bond pdb=" CA THR Y 782 " pdb=" CB THR Y 782 " ideal model delta sigma weight residual 1.526 1.497 0.030 1.53e-02 4.27e+03 3.75e+00 bond pdb=" CG1 ILE Y 79 " pdb=" CD1 ILE Y 79 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.86e+00 bond pdb=" C THR Y 279 " pdb=" N LEU Y 280 " ideal model delta sigma weight residual 1.331 1.296 0.035 2.07e-02 2.33e+03 2.82e+00 ... (remaining 11100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 15524 2.92 - 5.84: 281 5.84 - 8.76: 39 8.76 - 11.68: 6 11.68 - 14.60: 1 Bond angle restraints: 15851 Sorted by residual: angle pdb=" N SER Y 197 " pdb=" CA SER Y 197 " pdb=" C SER Y 197 " ideal model delta sigma weight residual 114.64 104.07 10.57 1.52e+00 4.33e-01 4.84e+01 angle pdb=" N GLY Y 572 " pdb=" CA GLY Y 572 " pdb=" C GLY Y 572 " ideal model delta sigma weight residual 113.18 127.78 -14.60 2.37e+00 1.78e-01 3.79e+01 angle pdb=" C ILE Y 198 " pdb=" N HIS Y 199 " pdb=" CA HIS Y 199 " ideal model delta sigma weight residual 121.54 133.12 -11.58 1.91e+00 2.74e-01 3.68e+01 angle pdb=" CA TRP Y 534 " pdb=" CB TRP Y 534 " pdb=" CG TRP Y 534 " ideal model delta sigma weight residual 113.60 124.37 -10.77 1.90e+00 2.77e-01 3.21e+01 angle pdb=" C SER Y 772 " pdb=" N ARG Y 773 " pdb=" CA ARG Y 773 " ideal model delta sigma weight residual 121.31 129.16 -7.85 1.49e+00 4.50e-01 2.77e+01 ... (remaining 15846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.26: 5926 34.26 - 68.51: 598 68.51 - 102.77: 53 102.77 - 137.03: 1 137.03 - 171.29: 4 Dihedral angle restraints: 6582 sinusoidal: 3925 harmonic: 2657 Sorted by residual: dihedral pdb=" O4' U B 17 " pdb=" C1' U B 17 " pdb=" N1 U B 17 " pdb=" C2 U B 17 " ideal model delta sinusoidal sigma weight residual 232.00 60.71 171.29 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" CA ILE Y 198 " pdb=" C ILE Y 198 " pdb=" N HIS Y 199 " pdb=" CA HIS Y 199 " ideal model delta harmonic sigma weight residual -180.00 -142.36 -37.64 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CA GLY Y 367 " pdb=" C GLY Y 367 " pdb=" N VAL Y 368 " pdb=" CA VAL Y 368 " ideal model delta harmonic sigma weight residual 180.00 -144.29 -35.71 0 5.00e+00 4.00e-02 5.10e+01 ... (remaining 6579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1566 0.066 - 0.133: 259 0.133 - 0.199: 44 0.199 - 0.265: 6 0.265 - 0.331: 5 Chirality restraints: 1880 Sorted by residual: chirality pdb=" C3' C B 40 " pdb=" C4' C B 40 " pdb=" O3' C B 40 " pdb=" C2' C B 40 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C3' G B 44 " pdb=" C4' G B 44 " pdb=" O3' G B 44 " pdb=" C2' G B 44 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C3' G B 60 " pdb=" C4' G B 60 " pdb=" O3' G B 60 " pdb=" C2' G B 60 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1877 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN Y 501 " 0.052 5.00e-02 4.00e+02 7.88e-02 9.94e+00 pdb=" N PRO Y 502 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO Y 502 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO Y 502 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE Y 609 " -0.021 2.00e-02 2.50e+03 1.95e-02 6.64e+00 pdb=" CG PHE Y 609 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE Y 609 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE Y 609 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE Y 609 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE Y 609 " -0.017 2.00e-02 2.50e+03 pdb=" CZ PHE Y 609 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 56 " 0.033 2.00e-02 2.50e+03 1.53e-02 6.40e+00 pdb=" N9 A B 56 " -0.035 2.00e-02 2.50e+03 pdb=" C8 A B 56 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A B 56 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A B 56 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A B 56 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A B 56 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A B 56 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A B 56 " -0.010 2.00e-02 2.50e+03 pdb=" N3 A B 56 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A B 56 " -0.002 2.00e-02 2.50e+03 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2526 2.79 - 3.32: 8775 3.32 - 3.85: 19254 3.85 - 4.37: 21458 4.37 - 4.90: 32711 Nonbonded interactions: 84724 Sorted by model distance: nonbonded pdb=" OH TYR Y 196 " pdb=" O SER Y 221 " model vdw 2.266 3.040 nonbonded pdb=" OG1 THR Y 684 " pdb=" O ASP Y 685 " model vdw 2.268 3.040 nonbonded pdb=" O SER Y 738 " pdb=" OG SER Y 738 " model vdw 2.297 3.040 nonbonded pdb=" OG1 THR Y 603 " pdb=" OP2 A B 18 " model vdw 2.306 3.040 nonbonded pdb=" ND2 ASN Y 549 " pdb=" O GLY Y 554 " model vdw 2.308 3.120 ... (remaining 84719 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 32.190 Find NCS groups from input model: 0.100 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.240 ------------------------------------------------------------------------------- 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 11105 Z= 0.429 Angle : 1.015 14.600 15851 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 *********************** 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 : 0.869 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: 0.3607 time to fit residues: 39.7153 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 : 0.916 ------------------------------------------------------------------------------- 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 = 0.118446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.088918 restraints weight = 22299.027| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.30 r_work: 0.3275 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 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 11105 Z= 0.180 Angle : 0.697 10.244 15851 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 *********************** 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 : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 86 GLU cc_start: 0.8630 (tp30) cc_final: 0.8389 (tp30) REVERT: Y 778 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8274 (tm-30) REVERT: Y 784 MET cc_start: 0.8872 (mmm) cc_final: 0.8199 (mmm) REVERT: Y 812 SER cc_start: 0.8701 (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: 0.8197 (t60) cc_final: 0.7621 (t60) outliers start: 15 outliers final: 9 residues processed: 88 average time/residue: 0.2604 time to fit residues: 32.0891 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 : 0.885 ------------------------------------------------------------------------------- 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: 5.9990 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: 6.9990 chunk 19 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.112160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.082093 restraints weight = 22855.328| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.32 r_work: 0.3151 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 11105 Z= 0.453 Angle : 0.822 11.738 15851 Z= 0.435 Chirality : 0.045 0.226 1880 Planarity : 0.005 0.042 1379 Dihedral : 24.446 168.038 3413 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.26 % Allowed : 16.88 % Favored : 82.86 % Rotamer: Outliers : 4.11 % Allowed : 17.11 % Favored : 78.78 % 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: -2.63 (0.29), residues: 782 helix: 0.27 (0.28), residues: 360 sheet: -2.56 (0.59), residues: 82 loop : -3.94 (0.26), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP Y 534 HIS 0.006 0.002 HIS Y 250 PHE 0.031 0.003 PHE Y 609 TYR 0.014 0.002 TYR Y 818 ARG 0.005 0.001 ARG Y 604 *********************** 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: 25 poor density : 55 time to evaluate : 0.869 Fit side-chains REVERT: Y 463 ASP cc_start: 0.8382 (m-30) cc_final: 0.8061 (m-30) REVERT: Y 736 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.6832 (p90) REVERT: Y 778 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8285 (tm-30) REVERT: Y 784 MET cc_start: 0.8902 (mmm) cc_final: 0.7921 (mmm) REVERT: Y 956 PHE cc_start: 0.7625 (t80) cc_final: 0.7396 (t80) REVERT: Y 970 TRP cc_start: 0.8302 (t60) cc_final: 0.7518 (t60) outliers start: 25 outliers final: 17 residues processed: 75 average time/residue: 0.2420 time to fit residues: 26.2204 Evaluate side-chains 65 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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: 6.9990 chunk 85 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 8 optimal weight: 0.0370 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 overall best weight: 1.6066 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.116270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.086566 restraints weight = 22481.251| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.29 r_work: 0.3239 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11105 Z= 0.213 Angle : 0.690 9.744 15851 Z= 0.368 Chirality : 0.039 0.220 1880 Planarity : 0.004 0.038 1379 Dihedral : 24.332 172.993 3413 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.47 % Favored : 84.40 % Rotamer: Outliers : 3.29 % Allowed : 19.41 % 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: -2.15 (0.30), residues: 782 helix: 0.69 (0.28), residues: 362 sheet: -2.53 (0.59), residues: 83 loop : -3.68 (0.27), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Y 534 HIS 0.015 0.002 HIS Y 91 PHE 0.022 0.002 PHE Y 503 TYR 0.012 0.001 TYR Y 818 ARG 0.003 0.000 ARG Y 753 *********************** 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: 20 poor density : 60 time to evaluate : 0.891 Fit side-chains REVERT: Y 463 ASP cc_start: 0.8407 (m-30) cc_final: 0.8177 (m-30) REVERT: Y 778 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8190 (tm-30) REVERT: Y 784 MET cc_start: 0.8824 (mmm) cc_final: 0.7935 (mmm) REVERT: Y 956 PHE cc_start: 0.7349 (t80) cc_final: 0.7103 (t80) REVERT: Y 970 TRP cc_start: 0.8225 (t60) cc_final: 0.7505 (t60) outliers start: 20 outliers final: 11 residues processed: 78 average time/residue: 0.2038 time to fit residues: 24.0442 Evaluate side-chains 67 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 67 MET Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 765 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 41 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.115095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.085173 restraints weight = 22537.429| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.29 r_work: 0.3213 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11105 Z= 0.270 Angle : 0.702 9.074 15851 Z= 0.375 Chirality : 0.040 0.222 1880 Planarity : 0.004 0.049 1379 Dihedral : 24.288 169.250 3413 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.98 % Favored : 83.89 % Rotamer: Outliers : 3.78 % Allowed : 18.59 % Favored : 77.63 % 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: -1.95 (0.30), residues: 782 helix: 0.91 (0.29), residues: 361 sheet: -2.49 (0.60), residues: 82 loop : -3.62 (0.27), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Y 534 HIS 0.004 0.001 HIS Y 250 PHE 0.015 0.002 PHE Y 503 TYR 0.012 0.002 TYR Y 818 ARG 0.002 0.000 ARG Y 604 *********************** 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 83 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.880 Fit side-chains REVERT: Y 265 ARG cc_start: 0.8536 (tmm-80) cc_final: 0.8122 (tmm-80) REVERT: Y 736 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7050 (p90) REVERT: Y 778 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8209 (tm-30) REVERT: Y 784 MET cc_start: 0.8845 (mmm) cc_final: 0.8049 (mmm) REVERT: Y 956 PHE cc_start: 0.7343 (t80) cc_final: 0.7108 (t80) REVERT: Y 970 TRP cc_start: 0.8224 (t60) cc_final: 0.7602 (t60) outliers start: 23 outliers final: 17 residues processed: 80 average time/residue: 0.2017 time to fit residues: 24.3360 Evaluate side-chains 72 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 57 ILE Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 583 ILE 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 Chi-restraints excluded: chain Y residue 967 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 11 optimal weight: 9.9990 chunk 71 optimal weight: 0.0980 chunk 72 optimal weight: 0.0070 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.118497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088792 restraints weight = 22531.890| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.32 r_work: 0.3279 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11105 Z= 0.185 Angle : 0.652 8.215 15851 Z= 0.349 Chirality : 0.038 0.218 1880 Planarity : 0.004 0.050 1379 Dihedral : 24.157 176.079 3413 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.35 % Favored : 84.65 % Rotamer: Outliers : 3.62 % Allowed : 18.59 % 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: -1.63 (0.31), residues: 782 helix: 1.14 (0.29), residues: 361 sheet: -2.22 (0.62), residues: 78 loop : -3.44 (0.28), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 758 PHE 0.012 0.001 PHE Y 98 TYR 0.022 0.001 TYR Y 711 ARG 0.003 0.000 ARG Y 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.857 Fit side-chains REVERT: Y 265 ARG cc_start: 0.8579 (tmm-80) cc_final: 0.8198 (tmm-80) REVERT: Y 736 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7240 (p90) REVERT: Y 766 LEU cc_start: 0.9161 (mt) cc_final: 0.8930 (mt) REVERT: Y 778 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8180 (tm-30) REVERT: Y 784 MET cc_start: 0.8396 (mmm) cc_final: 0.7930 (mmm) REVERT: Y 956 PHE cc_start: 0.7208 (t80) cc_final: 0.6956 (t80) REVERT: Y 970 TRP cc_start: 0.8173 (t60) cc_final: 0.7643 (t60) outliers start: 22 outliers final: 16 residues processed: 93 average time/residue: 0.2171 time to fit residues: 29.2411 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 : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 57 ILE 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 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 425 VAL Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 64 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 80 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.117459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.087896 restraints weight = 22811.477| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.33 r_work: 0.3265 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11105 Z= 0.206 Angle : 0.657 8.522 15851 Z= 0.351 Chirality : 0.038 0.219 1880 Planarity : 0.004 0.048 1379 Dihedral : 24.104 173.026 3413 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.47 % Favored : 84.53 % Rotamer: Outliers : 3.12 % Allowed : 21.22 % 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 (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: -1.56 (0.31), residues: 782 helix: 1.21 (0.29), residues: 362 sheet: -2.25 (0.62), residues: 78 loop : -3.41 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 758 PHE 0.014 0.002 PHE Y 775 TYR 0.012 0.001 TYR Y 818 ARG 0.002 0.000 ARG Y 265 *********************** 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 85 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.886 Fit side-chains REVERT: Y 265 ARG cc_start: 0.8602 (tmm-80) cc_final: 0.8306 (tmm-80) REVERT: Y 736 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7694 (p90) REVERT: Y 778 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8176 (tm-30) REVERT: Y 784 MET cc_start: 0.8761 (mmm) cc_final: 0.8158 (mmm) REVERT: Y 956 PHE cc_start: 0.7218 (t80) cc_final: 0.6966 (t80) REVERT: Y 970 TRP cc_start: 0.8192 (t60) cc_final: 0.7577 (t60) outliers start: 19 outliers final: 15 residues processed: 82 average time/residue: 0.2037 time to fit residues: 25.2566 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 : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 57 ILE 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 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 736 PHE Chi-restraints excluded: chain Y residue 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: 0.0770 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 overall best weight: 2.3342 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.116042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.086323 restraints weight = 22613.509| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.31 r_work: 0.3235 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11105 Z= 0.263 Angle : 0.688 9.172 15851 Z= 0.367 Chirality : 0.040 0.222 1880 Planarity : 0.004 0.044 1379 Dihedral : 24.102 170.769 3413 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.98 % Favored : 83.89 % Rotamer: Outliers : 3.12 % Allowed : 22.04 % 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: -1.60 (0.31), residues: 782 helix: 1.18 (0.29), residues: 362 sheet: -2.54 (0.60), residues: 82 loop : -3.36 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 758 PHE 0.027 0.002 PHE Y 775 TYR 0.013 0.002 TYR Y 818 ARG 0.003 0.000 ARG Y 753 *********************** 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: 19 poor density : 62 time to evaluate : 0.934 Fit side-chains REVERT: Y 265 ARG cc_start: 0.8603 (tmm-80) cc_final: 0.8291 (tmm-80) REVERT: Y 736 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.7647 (p90) REVERT: Y 778 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8253 (tm-30) REVERT: Y 784 MET cc_start: 0.8803 (mmm) cc_final: 0.8077 (mmm) REVERT: Y 956 PHE cc_start: 0.7247 (t80) cc_final: 0.7001 (t80) REVERT: Y 970 TRP cc_start: 0.8227 (t60) cc_final: 0.7604 (t60) outliers start: 19 outliers final: 17 residues processed: 77 average time/residue: 0.2059 time to fit residues: 23.5273 Evaluate side-chains 77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 57 ILE 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 343 TRP 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 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: 4.9990 chunk 45 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.119743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.090455 restraints weight = 22804.756| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.37 r_work: 0.3311 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11105 Z= 0.175 Angle : 0.650 8.253 15851 Z= 0.346 Chirality : 0.037 0.218 1880 Planarity : 0.004 0.046 1379 Dihedral : 23.981 178.641 3413 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.47 % Favored : 84.53 % Rotamer: Outliers : 3.12 % Allowed : 22.04 % 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: -1.42 (0.31), residues: 782 helix: 1.35 (0.29), residues: 362 sheet: -2.63 (0.60), residues: 85 loop : -3.25 (0.29), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Y 534 HIS 0.004 0.001 HIS Y 443 PHE 0.029 0.002 PHE Y 775 TYR 0.010 0.001 TYR Y 818 ARG 0.002 0.000 ARG Y 753 *********************** 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 85 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.916 Fit side-chains REVERT: Y 265 ARG cc_start: 0.8596 (tmm-80) cc_final: 0.8340 (tmm-80) REVERT: Y 736 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7946 (p90) REVERT: Y 747 MET cc_start: 0.8943 (tmm) cc_final: 0.8732 (tmm) REVERT: Y 778 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8244 (tm-30) REVERT: Y 784 MET cc_start: 0.8824 (mmm) cc_final: 0.8084 (mmm) REVERT: Y 970 TRP cc_start: 0.8177 (t60) cc_final: 0.7601 (t60) outliers start: 19 outliers final: 13 residues processed: 81 average time/residue: 0.1945 time to fit residues: 23.6819 Evaluate side-chains 76 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 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 736 PHE 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: 0.8980 chunk 30 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.116928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.087271 restraints weight = 22680.663| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.32 r_work: 0.3254 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11105 Z= 0.257 Angle : 0.689 9.150 15851 Z= 0.367 Chirality : 0.039 0.219 1880 Planarity : 0.004 0.041 1379 Dihedral : 23.999 170.915 3413 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.47 % Favored : 84.40 % Rotamer: Outliers : 2.47 % Allowed : 23.36 % Favored : 74.18 % 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: -1.43 (0.31), residues: 782 helix: 1.30 (0.29), residues: 362 sheet: -2.59 (0.61), residues: 80 loop : -3.20 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Y 534 HIS 0.003 0.001 HIS Y 758 PHE 0.040 0.002 PHE Y 775 TYR 0.013 0.002 TYR Y 575 ARG 0.002 0.000 ARG Y 753 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.883 Fit side-chains REVERT: Y 55 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7630 (mm-40) REVERT: Y 265 ARG cc_start: 0.8591 (tmm-80) cc_final: 0.8330 (tmm-80) REVERT: Y 736 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.7715 (p90) REVERT: Y 778 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8222 (tm-30) REVERT: Y 784 MET cc_start: 0.8806 (mmm) cc_final: 0.8007 (mmm) REVERT: Y 970 TRP cc_start: 0.8229 (t60) cc_final: 0.7547 (t60) outliers start: 15 outliers final: 12 residues processed: 75 average time/residue: 0.2195 time to fit residues: 24.6434 Evaluate side-chains 72 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 55 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 341 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 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: 1.9990 chunk 18 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.119316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.089876 restraints weight = 22616.917| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.34 r_work: 0.3299 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11105 Z= 0.182 Angle : 0.655 8.091 15851 Z= 0.349 Chirality : 0.037 0.218 1880 Planarity : 0.004 0.041 1379 Dihedral : 23.952 176.333 3413 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.86 % Favored : 84.14 % Rotamer: Outliers : 2.47 % Allowed : 23.36 % Favored : 74.18 % 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: -1.35 (0.31), residues: 782 helix: 1.46 (0.29), residues: 356 sheet: -2.64 (0.60), residues: 85 loop : -3.17 (0.29), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 443 PHE 0.033 0.002 PHE Y 775 TYR 0.011 0.001 TYR Y 818 ARG 0.006 0.000 ARG Y 777 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4869.63 seconds wall clock time: 87 minutes 9.16 seconds (5229.16 seconds total)