Starting phenix.real_space_refine on Fri Oct 23 02:22:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6n7w_0365/10_2026/6n7w_0365.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n7w_0365/10_2026/6n7w_0365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6n7w_0365/10_2026/6n7w_0365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n7w_0365/10_2026/6n7w_0365.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6n7w_0365/10_2026/6n7w_0365.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6n7w_0365/10_2026/6n7w_0365.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n7w_0365/10_2026/6n7w_0365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n7w_0365/10_2026/6n7w_0365.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians P 73 5.49 5 Mg 1 5.21 5 S 27 5.16 5 C 4755 2.51 5 N 1367 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7837 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5575 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 30, 'TRANS': 671} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 516 Unusual residues: {'2DA': 1} Classifications: {'DNA': 24, 'undetermined': 1} Link IDs: {'rna3p': 23, None: 1} Not linked: pdbres=" DG P 24 " pdbres="2DA P 25 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 918 Classifications: {'DNA': 45} Link IDs: {'rna3p': 44} Chain breaks: 1 Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.46, per 1000 atoms: 0.19 Number of scatterers: 7837 At special positions: 0 Unit cell: (98.04, 129, 103.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 P 73 15.00 Mg 1 11.99 O 1614 8.00 N 1367 7.00 C 4755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 230.0 milliseconds 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1480 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 52.0% alpha, 8.9% beta 32 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'H' and resid 35 through 37 No H-bonds generated for 'chain 'H' and resid 35 through 37' Processing helix chain 'H' and resid 38 through 52 Processing helix chain 'H' and resid 64 through 78 Processing helix chain 'H' and resid 91 through 99 Processing helix chain 'H' and resid 124 through 132 removed outlier: 3.519A pdb=" N TRP H 128 " --> pdb=" O ALA H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 151 Processing helix chain 'H' and resid 157 through 161 removed outlier: 3.573A pdb=" N TRP H 160 " --> pdb=" O GLY H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 186 Processing helix chain 'H' and resid 197 through 201 removed outlier: 4.100A pdb=" N VAL H 201 " --> pdb=" O PHE H 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 209 Processing helix chain 'H' and resid 211 through 231 removed outlier: 4.106A pdb=" N ASP H 215 " --> pdb=" O LEU H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 261 Processing helix chain 'H' and resid 303 through 308 Processing helix chain 'H' and resid 338 through 350 Processing helix chain 'H' and resid 365 through 372 Processing helix chain 'H' and resid 376 through 400 removed outlier: 4.402A pdb=" N ASP H 384 " --> pdb=" O GLN H 380 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 410 Processing helix chain 'H' and resid 436 through 440 removed outlier: 3.563A pdb=" N GLN H 439 " --> pdb=" O ASN H 436 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE H 440 " --> pdb=" O LEU H 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 436 through 440' Processing helix chain 'H' and resid 447 through 454 Processing helix chain 'H' and resid 456 through 460 removed outlier: 3.805A pdb=" N HIS H 459 " --> pdb=" O GLY H 456 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS H 460 " --> pdb=" O ALA H 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 456 through 460' Processing helix chain 'H' and resid 478 through 493 removed outlier: 4.980A pdb=" N ARG H 490 " --> pdb=" O HIS H 486 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N PHE H 491 " --> pdb=" O PHE H 487 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 500 Processing helix chain 'H' and resid 504 through 514 Processing helix chain 'H' and resid 517 through 530 Processing helix chain 'H' and resid 533 through 542 Processing helix chain 'H' and resid 544 through 559 Processing helix chain 'H' and resid 560 through 574 removed outlier: 3.751A pdb=" N ALA H 564 " --> pdb=" O PRO H 560 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL H 574 " --> pdb=" O GLN H 570 " (cutoff:3.500A) Processing helix chain 'H' and resid 608 through 636 removed outlier: 3.683A pdb=" N SER H 616 " --> pdb=" O THR H 612 " (cutoff:3.500A) Processing helix chain 'H' and resid 662 through 684 Processing helix chain 'H' and resid 699 through 704 Processing helix chain 'I' and resid 8 through 16 Processing helix chain 'I' and resid 34 through 49 Proline residue: I 40 - end of helix removed outlier: 3.640A pdb=" N ASP I 47 " --> pdb=" O ASP I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 71 Processing helix chain 'I' and resid 95 through 105 Processing sheet with id=AA1, first strand: chain 'H' and resid 31 through 32 removed outlier: 6.899A pdb=" N GLU H 7 " --> pdb=" O HIS H 19 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY H 21 " --> pdb=" O ASP H 5 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP H 5 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE H 23 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL H 3 " --> pdb=" O ILE H 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 264 through 266 Processing sheet with id=AA3, first strand: chain 'H' and resid 327 through 328 Processing sheet with id=AA4, first strand: chain 'H' and resid 420 through 421 Processing sheet with id=AA5, first strand: chain 'H' and resid 648 through 650 removed outlier: 3.522A pdb=" N MET H 649 " --> pdb=" O GLN H 657 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN H 657 " --> pdb=" O MET H 649 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL H 470 " --> pdb=" O CYS H 660 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 576 through 577 Processing sheet with id=AA7, first strand: chain 'H' and resid 592 through 594 Processing sheet with id=AA8, first strand: chain 'I' and resid 5 through 6 removed outlier: 6.583A pdb=" N ILE I 5 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ASN I 59 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE I 27 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR I 77 " --> pdb=" O PHE I 27 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA I 88 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LYS I 82 " --> pdb=" O VAL I 86 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL I 86 " --> pdb=" O LYS I 82 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 912 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1185 1.31 - 1.43: 2512 1.43 - 1.56: 4281 1.56 - 1.68: 141 1.68 - 1.81: 42 Bond restraints: 8161 Sorted by residual: bond pdb=" C6 TTP H4002 " pdb=" N1 TTP H4002 " ideal model delta sigma weight residual 1.337 1.427 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" P 2DA P 25 " pdb=" O5' 2DA P 25 " ideal model delta sigma weight residual 1.730 1.648 0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C2 TTP H4002 " pdb=" N1 TTP H4002 " ideal model delta sigma weight residual 1.410 1.488 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" N THR H 16 " pdb=" CA THR H 16 " ideal model delta sigma weight residual 1.458 1.488 -0.030 9.00e-03 1.23e+04 1.13e+01 bond pdb=" C3' DC P 21 " pdb=" C2' DC P 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 8156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 11181 2.49 - 4.98: 141 4.98 - 7.46: 21 7.46 - 9.95: 6 9.95 - 12.44: 4 Bond angle restraints: 11353 Sorted by residual: angle pdb=" O4' DG T 49 " pdb=" C4' DG T 49 " pdb=" C3' DG T 49 " ideal model delta sigma weight residual 106.00 103.10 2.90 6.00e-01 2.78e+00 2.33e+01 angle pdb=" C HIS H 653 " pdb=" N ASP H 654 " pdb=" CA ASP H 654 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" N3 DT P 23 " pdb=" C4 DT P 23 " pdb=" O4 DT P 23 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT T 66 " pdb=" C4 DT T 66 " pdb=" O4 DT T 66 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" O4' DA P 19 " pdb=" C4' DA P 19 " pdb=" C3' DA P 19 " ideal model delta sigma weight residual 106.00 103.40 2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 11348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.21: 4219 30.21 - 60.42: 410 60.42 - 90.63: 16 90.63 - 120.84: 1 120.84 - 151.05: 1 Dihedral angle restraints: 4647 sinusoidal: 2335 harmonic: 2312 Sorted by residual: dihedral pdb=" C2 TTP H4002 " pdb=" C1' TTP H4002 " pdb=" N1 TTP H4002 " pdb=" O4' TTP H4002 " ideal model delta sinusoidal sigma weight residual 301.68 150.63 151.05 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" CA GLY I 33 " pdb=" C GLY I 33 " pdb=" N PRO I 34 " pdb=" CA PRO I 34 " ideal model delta harmonic sigma weight residual 180.00 150.76 29.24 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" O3B TTP H4002 " pdb=" O3A TTP H4002 " pdb=" PB TTP H4002 " pdb=" PA TTP H4002 " ideal model delta sinusoidal sigma weight residual 180.00 67.20 112.80 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 4644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 902 0.050 - 0.100: 255 0.100 - 0.150: 63 0.150 - 0.199: 4 0.199 - 0.249: 3 Chirality restraints: 1227 Sorted by residual: chirality pdb=" C3' TTP H4002 " pdb=" C2' TTP H4002 " pdb=" C4' TTP H4002 " pdb=" O3' TTP H4002 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C1' 2DA P 25 " pdb=" O4' 2DA P 25 " pdb=" C2' 2DA P 25 " pdb=" N9 2DA P 25 " both_signs ideal model delta sigma weight residual False 2.38 2.62 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C4' TTP H4002 " pdb=" C3' TTP H4002 " pdb=" C5' TTP H4002 " pdb=" O4' TTP H4002 " both_signs ideal model delta sigma weight residual False -2.50 -2.71 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1224 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 52 " 0.732 9.50e-02 1.11e+02 3.28e-01 6.55e+01 pdb=" NE ARG H 52 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG H 52 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG H 52 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 52 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 307 " -0.695 9.50e-02 1.11e+02 3.11e-01 5.91e+01 pdb=" NE ARG H 307 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG H 307 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG H 307 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 307 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 96 " -0.491 9.50e-02 1.11e+02 2.20e-01 2.96e+01 pdb=" NE ARG H 96 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG H 96 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG H 96 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 96 " -0.017 2.00e-02 2.50e+03 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 155 2.68 - 3.24: 6503 3.24 - 3.79: 13125 3.79 - 4.35: 16487 4.35 - 4.90: 25353 Nonbonded interactions: 61623 Sorted by model distance: nonbonded pdb=" OD2 ASP H 654 " pdb="MG MG H4001 " model vdw 2.125 2.170 nonbonded pdb=" O SER H 568 " pdb=" OG1 THR H 572 " model vdw 2.290 3.040 nonbonded pdb=" O ALA H 476 " pdb="MG MG H4001 " model vdw 2.294 2.170 nonbonded pdb="MG MG H4001 " pdb=" O3G TTP H4002 " model vdw 2.329 2.170 nonbonded pdb=" OG SER H 4 " pdb=" OH TYR H 42 " model vdw 2.361 3.040 ... (remaining 61618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.550 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 0.005 0.090 8162 Z= 0.382 Angle : 0.817 12.438 11353 Z= 0.568 Chirality : 0.048 0.249 1227 Planarity : 0.016 0.328 1218 Dihedral : 19.448 151.054 3167 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.36 % Favored : 95.51 % Rotamer: Outliers : 0.46 % Allowed : 3.50 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.26), residues: 802 helix: -1.57 (0.20), residues: 392 sheet: -0.88 (0.69), residues: 69 loop : -1.86 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 591 TYR 0.013 0.001 TYR H 326 PHE 0.016 0.002 PHE H 487 TRP 0.019 0.002 TRP H 679 HIS 0.005 0.001 HIS H 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.38 ( 8161) covalent geometry : angle 0.81720 / 0.57 (11353) hydrogen bonds : bond 0.12234 / 8.44 ( 393) hydrogen bonds : angle 5.61971 / 3.83 ( 1074) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LEU cc_start: 0.9158 (mt) cc_final: 0.8636 (mm) REVERT: H 135 MET cc_start: 0.7843 (tpp) cc_final: 0.5030 (mmm) REVERT: H 167 MET cc_start: 0.9306 (ttm) cc_final: 0.9073 (ttp) REVERT: H 488 MET cc_start: 0.8127 (ptt) cc_final: 0.7184 (ppp) REVERT: H 658 VAL cc_start: 0.9124 (t) cc_final: 0.8886 (m) REVERT: I 23 ILE cc_start: 0.9004 (mt) cc_final: 0.8768 (mm) REVERT: I 57 LYS cc_start: 0.9180 (mtpt) cc_final: 0.8770 (mtpp) REVERT: I 70 TYR cc_start: 0.8101 (m-80) cc_final: 0.7700 (m-80) outliers start: 3 outliers final: 0 residues processed: 150 average time/residue: 0.1062 time to fit residues: 20.3327 Evaluate side-chains 70 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 62 HIS H 173 GLN H 190 HIS H 227 GLN H 423 ASN H 520 ASN H 570 GLN H 615 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.061896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.047285 restraints weight = 41673.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.048543 restraints weight = 23382.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.049345 restraints weight = 15794.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.049917 restraints weight = 12170.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.050172 restraints weight = 10202.525| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8162 Z= 0.226 Angle : 0.687 8.237 11353 Z= 0.375 Chirality : 0.044 0.200 1227 Planarity : 0.005 0.055 1218 Dihedral : 23.867 145.712 1647 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.15 % Allowed : 1.52 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.30), residues: 802 helix: 0.49 (0.26), residues: 394 sheet: -0.27 (0.68), residues: 68 loop : -1.29 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 35 TYR 0.022 0.002 TYR H 203 PHE 0.033 0.002 PHE H 686 TRP 0.015 0.002 TRP H 651 HIS 0.006 0.001 HIS H 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.23 ( 8161) covalent geometry : angle 0.68710 / 0.37 (11353) hydrogen bonds : bond 0.04794 / 3.18 ( 393) hydrogen bonds : angle 4.75858 / 3.22 ( 1074) Misc. bond : bond 0.00152 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 107 MET cc_start: 0.9200 (mpp) cc_final: 0.8917 (mpp) REVERT: H 189 LYS cc_start: 0.8973 (tmtt) cc_final: 0.8772 (tptp) REVERT: H 488 MET cc_start: 0.8456 (ptt) cc_final: 0.7025 (ppp) REVERT: H 677 MET cc_start: 0.8932 (tpp) cc_final: 0.8451 (tpp) REVERT: I 23 ILE cc_start: 0.9049 (mt) cc_final: 0.8830 (mm) REVERT: I 69 LYS cc_start: 0.9147 (ptpp) cc_final: 0.8550 (pttt) REVERT: I 70 TYR cc_start: 0.8583 (m-80) cc_final: 0.8003 (m-80) REVERT: I 100 LYS cc_start: 0.9419 (ptpt) cc_final: 0.9186 (mtmm) outliers start: 1 outliers final: 1 residues processed: 89 average time/residue: 0.1117 time to fit residues: 12.8825 Evaluate side-chains 53 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [15, 43, 74, 23, 9, 33, 55, 38, 26, 17, 13] chunk 15 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 55 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.061851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.047497 restraints weight = 41372.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.048798 restraints weight = 23085.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.049632 restraints weight = 15447.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.050212 restraints weight = 11794.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.050466 restraints weight = 9818.200| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8162 Z= 0.133 Angle : 0.564 7.760 11353 Z= 0.316 Chirality : 0.042 0.181 1227 Planarity : 0.004 0.052 1218 Dihedral : 23.884 146.183 1647 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.31), residues: 802 helix: 1.13 (0.27), residues: 395 sheet: -0.10 (0.64), residues: 68 loop : -1.03 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 73 TYR 0.016 0.001 TYR H 203 PHE 0.017 0.001 PHE H 686 TRP 0.012 0.001 TRP H 651 HIS 0.004 0.001 HIS H 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 8161) covalent geometry : angle 0.56440 / 0.32 (11353) hydrogen bonds : bond 0.03978 / 2.61 ( 393) hydrogen bonds : angle 4.34743 / 2.97 ( 1074) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 ILE cc_start: 0.9552 (pt) cc_final: 0.9219 (pt) REVERT: H 107 MET cc_start: 0.9172 (mpp) cc_final: 0.8842 (mpp) REVERT: H 189 LYS cc_start: 0.8932 (tmtt) cc_final: 0.8707 (tptp) REVERT: H 488 MET cc_start: 0.8369 (ptt) cc_final: 0.7083 (ppp) REVERT: H 677 MET cc_start: 0.9059 (tpp) cc_final: 0.8589 (tpp) REVERT: H 696 MET cc_start: 0.7061 (tmm) cc_final: 0.6821 (tmm) REVERT: I 70 TYR cc_start: 0.8476 (m-80) cc_final: 0.7818 (m-80) REVERT: I 85 GLU cc_start: 0.7859 (pm20) cc_final: 0.7649 (pm20) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0983 time to fit residues: 10.2082 Evaluate side-chains 58 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [69, 46, 39, 83, 16, 11, 38, 71, 33, 36, 51] chunk 69 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 150 GLN H 227 GLN H 459 HIS H 520 ASN H 653 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.059710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.045244 restraints weight = 43330.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.046446 restraints weight = 24359.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.047246 restraints weight = 16523.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.047667 restraints weight = 12811.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.048084 restraints weight = 11014.079| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8162 Z= 0.195 Angle : 0.633 7.781 11353 Z= 0.346 Chirality : 0.043 0.177 1227 Planarity : 0.004 0.051 1218 Dihedral : 23.916 147.636 1647 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.15 % Allowed : 2.44 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 2.86 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.31), residues: 802 helix: 1.23 (0.27), residues: 393 sheet: 0.04 (0.63), residues: 64 loop : -0.89 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 73 TYR 0.013 0.002 TYR H 203 PHE 0.011 0.001 PHE H 686 TRP 0.016 0.002 TRP H 651 HIS 0.007 0.002 HIS H 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.20 ( 8161) covalent geometry : angle 0.63320 / 0.35 (11353) hydrogen bonds : bond 0.04818 / 3.22 ( 393) hydrogen bonds : angle 4.42676 / 3.06 ( 1074) Misc. bond : bond 0.00066 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 ILE cc_start: 0.9377 (pt) cc_final: 0.8997 (mt) REVERT: H 107 MET cc_start: 0.9190 (mpp) cc_final: 0.8896 (mpp) REVERT: H 135 MET cc_start: 0.7715 (mmm) cc_final: 0.7511 (mmm) REVERT: H 170 TYR cc_start: 0.7176 (t80) cc_final: 0.6871 (t80) REVERT: H 174 ASP cc_start: 0.8738 (m-30) cc_final: 0.8143 (m-30) REVERT: H 189 LYS cc_start: 0.9067 (tmtt) cc_final: 0.8837 (tptp) REVERT: H 488 MET cc_start: 0.8013 (ptt) cc_final: 0.6796 (ppp) REVERT: H 677 MET cc_start: 0.8961 (tpp) cc_final: 0.8434 (tpp) REVERT: I 69 LYS cc_start: 0.9099 (ptpp) cc_final: 0.8564 (pttt) REVERT: I 70 TYR cc_start: 0.8502 (m-80) cc_final: 0.7929 (m-80) outliers start: 1 outliers final: 0 residues processed: 73 average time/residue: 0.0979 time to fit residues: 9.5775 Evaluate side-chains 59 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [72, 47, 20, 19, 48, 29, 6, 22, 75, 35, 54] chunk 72 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.0370 chunk 48 optimal weight: 0.0020 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.5066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.060521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.045845 restraints weight = 42607.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.047095 restraints weight = 23613.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.047930 restraints weight = 15935.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.048525 restraints weight = 12205.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.048911 restraints weight = 10138.629| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8162 Z= 0.126 Angle : 0.560 7.515 11353 Z= 0.314 Chirality : 0.041 0.172 1227 Planarity : 0.004 0.056 1218 Dihedral : 23.938 146.830 1647 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.31), residues: 802 helix: 1.46 (0.27), residues: 393 sheet: -0.27 (0.60), residues: 76 loop : -0.70 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 255 TYR 0.013 0.001 TYR H 139 PHE 0.011 0.001 PHE H 686 TRP 0.013 0.001 TRP H 651 HIS 0.005 0.001 HIS H 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 ( 8161) covalent geometry : angle 0.55993 / 0.31 (11353) hydrogen bonds : bond 0.04064 / 2.68 ( 393) hydrogen bonds : angle 4.19649 / 2.88 ( 1074) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 ILE cc_start: 0.9543 (pt) cc_final: 0.9190 (mt) REVERT: H 107 MET cc_start: 0.9282 (mpp) cc_final: 0.8867 (mpp) REVERT: H 119 ARG cc_start: 0.8427 (mmt180) cc_final: 0.8041 (mmm-85) REVERT: H 135 MET cc_start: 0.7336 (mmm) cc_final: 0.6997 (mmm) REVERT: H 167 MET cc_start: 0.9112 (mtm) cc_final: 0.8604 (mtm) REVERT: H 170 TYR cc_start: 0.7153 (t80) cc_final: 0.6803 (t80) REVERT: H 174 ASP cc_start: 0.8677 (m-30) cc_final: 0.8075 (m-30) REVERT: H 189 LYS cc_start: 0.9048 (tmtt) cc_final: 0.8774 (tptp) REVERT: H 488 MET cc_start: 0.8007 (ptt) cc_final: 0.6749 (ppp) REVERT: H 649 MET cc_start: 0.8675 (pmm) cc_final: 0.8467 (pmm) REVERT: H 677 MET cc_start: 0.9075 (tpp) cc_final: 0.8640 (tpp) REVERT: I 69 LYS cc_start: 0.9169 (ptpp) cc_final: 0.8757 (pttt) REVERT: I 70 TYR cc_start: 0.8435 (m-80) cc_final: 0.7886 (m-80) REVERT: I 100 LYS cc_start: 0.9385 (ptpt) cc_final: 0.9131 (mtmt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0885 time to fit residues: 8.7527 Evaluate side-chains 55 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [12, 29, 77, 75, 32, 55, 0, 65, 6, 76, 33] chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 303 ASN H 520 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.058454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.044042 restraints weight = 43085.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.045202 restraints weight = 24153.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.045923 restraints weight = 16475.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.046467 restraints weight = 12890.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.046762 restraints weight = 10870.436| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8162 Z= 0.192 Angle : 0.626 7.634 11353 Z= 0.338 Chirality : 0.042 0.167 1227 Planarity : 0.004 0.056 1218 Dihedral : 23.956 148.459 1647 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.31), residues: 802 helix: 1.43 (0.27), residues: 393 sheet: -0.33 (0.61), residues: 78 loop : -0.62 (0.37), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 255 TYR 0.009 0.002 TYR H 191 PHE 0.012 0.001 PHE H 686 TRP 0.018 0.002 TRP H 469 HIS 0.008 0.002 HIS H 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 ( 8161) covalent geometry : angle 0.62551 / 0.34 (11353) hydrogen bonds : bond 0.04922 / 3.28 ( 393) hydrogen bonds : angle 4.35685 / 3.03 ( 1074) Misc. bond : bond 0.00052 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 ILE cc_start: 0.9510 (pt) cc_final: 0.9048 (mt) REVERT: H 107 MET cc_start: 0.9297 (mpp) cc_final: 0.8887 (mpp) REVERT: H 135 MET cc_start: 0.7390 (mmm) cc_final: 0.7074 (mmm) REVERT: H 167 MET cc_start: 0.9131 (mtm) cc_final: 0.8764 (mtp) REVERT: H 170 TYR cc_start: 0.7172 (t80) cc_final: 0.6872 (t80) REVERT: H 174 ASP cc_start: 0.8725 (m-30) cc_final: 0.8117 (m-30) REVERT: H 488 MET cc_start: 0.8130 (ptt) cc_final: 0.7827 (ppp) REVERT: H 677 MET cc_start: 0.9001 (tpp) cc_final: 0.8444 (tpp) REVERT: I 69 LYS cc_start: 0.9110 (ptpp) cc_final: 0.8759 (pmtt) REVERT: I 100 LYS cc_start: 0.9410 (ptpt) cc_final: 0.9194 (mtmm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0967 time to fit residues: 8.3686 Evaluate side-chains 49 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [35, 37, 45, 63, 74, 40, 5, 82, 16, 20, 70] chunk 35 optimal weight: 0.0970 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 82 optimal weight: 20.0000 chunk 16 optimal weight: 0.0870 chunk 20 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.059825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.045165 restraints weight = 42830.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.046379 restraints weight = 23889.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.047179 restraints weight = 16172.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.047725 restraints weight = 12463.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.047990 restraints weight = 10507.944| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8162 Z= 0.115 Angle : 0.547 7.384 11353 Z= 0.306 Chirality : 0.041 0.164 1227 Planarity : 0.004 0.055 1218 Dihedral : 23.959 146.867 1647 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.31), residues: 802 helix: 1.66 (0.27), residues: 393 sheet: -0.14 (0.61), residues: 78 loop : -0.60 (0.37), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 255 TYR 0.010 0.001 TYR H 203 PHE 0.010 0.001 PHE H 163 TRP 0.011 0.001 TRP H 469 HIS 0.006 0.001 HIS H 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.12 ( 8161) covalent geometry : angle 0.54667 / 0.31 (11353) hydrogen bonds : bond 0.03978 / 2.60 ( 393) hydrogen bonds : angle 4.14455 / 2.84 ( 1074) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 ILE cc_start: 0.9493 (pt) cc_final: 0.9025 (mt) REVERT: H 107 MET cc_start: 0.9272 (mpp) cc_final: 0.8836 (mpp) REVERT: H 119 ARG cc_start: 0.8479 (mmt180) cc_final: 0.8062 (mmm-85) REVERT: H 135 MET cc_start: 0.7324 (mmm) cc_final: 0.7007 (mmm) REVERT: H 167 MET cc_start: 0.9205 (mtm) cc_final: 0.8553 (mtp) REVERT: H 170 TYR cc_start: 0.7075 (t80) cc_final: 0.6733 (t80) REVERT: H 174 ASP cc_start: 0.8713 (m-30) cc_final: 0.8058 (m-30) REVERT: H 488 MET cc_start: 0.7992 (ptt) cc_final: 0.6732 (ppp) REVERT: H 649 MET cc_start: 0.8674 (pmm) cc_final: 0.7946 (pmm) REVERT: H 677 MET cc_start: 0.9024 (tpp) cc_final: 0.8547 (tpp) REVERT: H 686 PHE cc_start: 0.7989 (t80) cc_final: 0.7651 (t80) REVERT: H 696 MET cc_start: 0.7512 (tmm) cc_final: 0.6915 (tmm) REVERT: I 44 GLU cc_start: 0.8881 (pt0) cc_final: 0.8665 (tm-30) REVERT: I 100 LYS cc_start: 0.9412 (ptpt) cc_final: 0.9144 (mtmt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0842 time to fit residues: 7.7176 Evaluate side-chains 52 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [7, 44, 0, 68, 59, 63, 56, 19, 23, 8, 74] chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 0.0170 chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.059474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.044821 restraints weight = 42529.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.046055 restraints weight = 23525.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.046879 restraints weight = 15883.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.047252 restraints weight = 12181.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.047694 restraints weight = 10537.297| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8162 Z= 0.133 Angle : 0.561 7.329 11353 Z= 0.313 Chirality : 0.041 0.162 1227 Planarity : 0.004 0.057 1218 Dihedral : 23.902 147.095 1647 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.31), residues: 802 helix: 1.65 (0.27), residues: 393 sheet: -0.08 (0.61), residues: 78 loop : -0.58 (0.37), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 255 TYR 0.009 0.001 TYR H 203 PHE 0.010 0.001 PHE H 686 TRP 0.011 0.001 TRP H 651 HIS 0.006 0.001 HIS H 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 ( 8161) covalent geometry : angle 0.56054 / 0.31 (11353) hydrogen bonds : bond 0.04001 / 2.64 ( 393) hydrogen bonds : angle 4.20529 / 2.92 ( 1074) Misc. bond : bond 0.00054 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 ILE cc_start: 0.9515 (pt) cc_final: 0.9063 (mt) REVERT: H 119 ARG cc_start: 0.8497 (mmt180) cc_final: 0.8075 (mmm-85) REVERT: H 135 MET cc_start: 0.7354 (mmm) cc_final: 0.7027 (mmm) REVERT: H 167 MET cc_start: 0.9239 (mtm) cc_final: 0.8692 (mtp) REVERT: H 170 TYR cc_start: 0.7080 (t80) cc_final: 0.6812 (t80) REVERT: H 174 ASP cc_start: 0.8716 (m-30) cc_final: 0.8079 (m-30) REVERT: H 677 MET cc_start: 0.9099 (tpp) cc_final: 0.8616 (tpp) REVERT: H 686 PHE cc_start: 0.8020 (t80) cc_final: 0.7660 (t80) REVERT: H 696 MET cc_start: 0.7392 (tmm) cc_final: 0.6849 (tmm) REVERT: I 30 GLU cc_start: 0.8156 (pp20) cc_final: 0.7655 (pp20) REVERT: I 44 GLU cc_start: 0.8883 (pt0) cc_final: 0.8671 (tm-30) REVERT: I 66 THR cc_start: 0.8720 (m) cc_final: 0.8440 (m) REVERT: I 69 LYS cc_start: 0.9167 (pttm) cc_final: 0.8840 (pttp) REVERT: I 100 LYS cc_start: 0.9373 (ptpt) cc_final: 0.9094 (mtmt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1006 time to fit residues: 9.0981 Evaluate side-chains 53 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [17, 58, 0, 50, 44, 1, 21, 45, 24, 30, 38] chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 0.0970 chunk 44 optimal weight: 0.0670 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 30 optimal weight: 0.0270 chunk 38 optimal weight: 2.9990 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.060423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.045685 restraints weight = 41619.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.046971 restraints weight = 22825.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.047817 restraints weight = 15178.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.048353 restraints weight = 11560.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.048612 restraints weight = 9710.332| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8162 Z= 0.110 Angle : 0.542 7.165 11353 Z= 0.303 Chirality : 0.041 0.184 1227 Planarity : 0.004 0.055 1218 Dihedral : 23.843 146.469 1647 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.31), residues: 802 helix: 1.76 (0.27), residues: 393 sheet: 0.09 (0.62), residues: 78 loop : -0.53 (0.37), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 255 TYR 0.010 0.001 TYR H 203 PHE 0.009 0.001 PHE H 686 TRP 0.009 0.001 TRP H 651 HIS 0.004 0.001 HIS H 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.11 ( 8161) covalent geometry : angle 0.54220 / 0.30 (11353) hydrogen bonds : bond 0.03636 / 2.38 ( 393) hydrogen bonds : angle 4.01385 / 2.79 ( 1074) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 ILE cc_start: 0.9514 (pt) cc_final: 0.9073 (mt) REVERT: H 107 MET cc_start: 0.9283 (mpp) cc_final: 0.8853 (mpp) REVERT: H 135 MET cc_start: 0.7311 (mmm) cc_final: 0.6956 (mmm) REVERT: H 158 MET cc_start: 0.9199 (mmm) cc_final: 0.8797 (mmm) REVERT: H 167 MET cc_start: 0.9250 (mtm) cc_final: 0.8661 (mtp) REVERT: H 170 TYR cc_start: 0.7025 (t80) cc_final: 0.6775 (t80) REVERT: H 174 ASP cc_start: 0.8720 (m-30) cc_final: 0.8058 (m-30) REVERT: H 488 MET cc_start: 0.7471 (ppp) cc_final: 0.6392 (ppp) REVERT: H 677 MET cc_start: 0.9053 (tpp) cc_final: 0.8542 (tpp) REVERT: H 686 PHE cc_start: 0.8033 (t80) cc_final: 0.7647 (t80) REVERT: H 696 MET cc_start: 0.7483 (tmm) cc_final: 0.7014 (tmm) REVERT: I 69 LYS cc_start: 0.9227 (pttm) cc_final: 0.8826 (pttp) REVERT: I 100 LYS cc_start: 0.9367 (ptpt) cc_final: 0.9097 (mtmt) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0908 time to fit residues: 8.9292 Evaluate side-chains 56 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [17, 5, 16, 58, 83, 33, 60, 39, 77, 48, 69] chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.059089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.045089 restraints weight = 41605.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.046284 restraints weight = 23316.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.047083 restraints weight = 15715.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.047603 restraints weight = 12004.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.047890 restraints weight = 10049.844| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8162 Z= 0.141 Angle : 0.561 7.241 11353 Z= 0.311 Chirality : 0.042 0.159 1227 Planarity : 0.004 0.055 1218 Dihedral : 23.812 147.329 1647 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.31), residues: 802 helix: 1.75 (0.27), residues: 393 sheet: 0.11 (0.63), residues: 70 loop : -0.61 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 255 TYR 0.008 0.001 TYR H 203 PHE 0.010 0.001 PHE H 686 TRP 0.010 0.001 TRP H 700 HIS 0.005 0.001 HIS H 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 8161) covalent geometry : angle 0.56111 / 0.31 (11353) hydrogen bonds : bond 0.03942 / 2.58 ( 393) hydrogen bonds : angle 4.13136 / 2.87 ( 1074) Misc. bond : bond 0.00052 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1604 Ramachandran restraints generated. 802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 2 ILE cc_start: 0.9480 (pt) cc_final: 0.9082 (mt) REVERT: H 107 MET cc_start: 0.9286 (mpp) cc_final: 0.8865 (mpp) REVERT: H 119 ARG cc_start: 0.8538 (mmt180) cc_final: 0.8212 (mmm-85) REVERT: H 135 MET cc_start: 0.7346 (mmm) cc_final: 0.7008 (mmm) REVERT: H 167 MET cc_start: 0.9253 (mtm) cc_final: 0.8660 (mtp) REVERT: H 170 TYR cc_start: 0.6993 (t80) cc_final: 0.6717 (t80) REVERT: H 174 ASP cc_start: 0.8690 (m-30) cc_final: 0.8041 (m-30) REVERT: H 488 MET cc_start: 0.7612 (ppp) cc_final: 0.6621 (ppp) REVERT: H 677 MET cc_start: 0.9070 (tpp) cc_final: 0.8567 (tpp) REVERT: H 686 PHE cc_start: 0.8041 (t80) cc_final: 0.7616 (t80) REVERT: I 69 LYS cc_start: 0.9155 (pttm) cc_final: 0.8865 (pttp) REVERT: I 100 LYS cc_start: 0.9370 (ptpt) cc_final: 0.9137 (mtmm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0923 time to fit residues: 8.2034 Evaluate side-chains 50 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: [53, 84, 58, 47, 33, 81, 82, 3, 76, 61, 44] chunk 53 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 439 GLN H 520 ASN H 640 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.056668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.042335 restraints weight = 42658.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.043461 restraints weight = 24384.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.044209 restraints weight = 16774.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.044639 restraints weight = 13020.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.044985 restraints weight = 11147.836| |-----------------------------------------------------------------------------| r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8162 Z= 0.221 Angle : 0.679 9.117 11353 Z= 0.362 Chirality : 0.044 0.160 1227 Planarity : 0.004 0.050 1218 Dihedral : 23.958 148.913 1647 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.31), residues: 802 helix: 1.56 (0.26), residues: 394 sheet: -0.06 (0.66), residues: 59 loop : -0.73 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 288 TYR 0.012 0.002 TYR H 191 PHE 0.016 0.002 PHE I 12 TRP 0.027 0.002 TRP H 469 HIS 0.010 0.002 HIS H 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.22 ( 8161) covalent geometry : angle 0.67894 / 0.36 (11353) hydrogen bonds : bond 0.05251 / 3.45 ( 393) hydrogen bonds : angle 4.50017 / 3.13 ( 1074) Misc. bond : bond 0.00086 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1249.04 seconds wall clock time: 22 minutes 40.97 seconds (1360.97 seconds total)