Starting phenix.real_space_refine on Sat Dec 28 01:09:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u2a_26310/12_2024/7u2a_26310.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2a_26310/12_2024/7u2a_26310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7u2a_26310/12_2024/7u2a_26310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2a_26310/12_2024/7u2a_26310.map" model { file = "/net/cci-nas-00/data/ceres_data/7u2a_26310/12_2024/7u2a_26310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2a_26310/12_2024/7u2a_26310.cif" } resolution = 4.1 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= -0.000 sd= 0.010 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 38 5.49 5 S 34 5.16 5 C 4179 2.51 5 N 1233 2.21 5 O 1371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6855 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 794 Classifications: {'RNA': 38} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 15, 'rna3p_pyr': 20} Link IDs: {'rna2p': 2, 'rna3p': 35} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {' A%rna2p_pur:plan2': 1, ' A%rna2p_pur:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2500 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3503 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 415} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'SSA%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'SSA%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 4.79, per 1000 atoms: 0.70 Number of scatterers: 6855 At special positions: 0 Unit cell: (70.15, 83.95, 117.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 38 15.00 O 1371 8.00 N 1233 7.00 C 4179 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=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 712.9 milliseconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 7 sheets defined 42.2% alpha, 16.7% beta 10 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 220 through 225 Processing helix chain 'A' and resid 233 through 253 Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 299 through 308 removed outlier: 4.156A pdb=" N GLY A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 383 Processing helix chain 'A' and resid 428 through 434 Processing helix chain 'A' and resid 457 through 468 Processing helix chain 'A' and resid 478 through 486 removed outlier: 4.296A pdb=" N SER A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N TYR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.737A pdb=" N GLU B 46 " --> pdb=" O ASN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 65 removed outlier: 4.354A pdb=" N ALA B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 78 removed outlier: 3.605A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 85 through 118 removed outlier: 3.724A pdb=" N ILE B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 169 Proline residue: B 154 - end of helix removed outlier: 4.233A pdb=" N LYS B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 233 through 254 Processing helix chain 'B' and resid 266 through 273 Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.888A pdb=" N GLY B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 383 Processing helix chain 'B' and resid 392 through 397 removed outlier: 4.546A pdb=" N GLY B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 434 removed outlier: 3.546A pdb=" N ARG B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 469 Processing helix chain 'B' and resid 478 through 486 removed outlier: 3.813A pdb=" N SER B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 192 removed outlier: 6.262A pdb=" N ARG A 402 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER A 423 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE A 404 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 421 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 406 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 417 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N VAL A 419 " --> pdb=" O CYS A 455 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS A 455 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER A 421 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR A 453 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN A 451 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 449 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS A 448 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL A 351 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA A 456 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR A 349 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 350 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER A 326 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER A 325 " --> pdb=" O MET A 258 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 231 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 216 removed outlier: 3.735A pdb=" N TYR A 230 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 231 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER B 325 " --> pdb=" O MET B 258 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER B 326 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 350 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR B 349 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ALA B 456 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL B 351 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER B 421 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N CYS B 455 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N VAL B 419 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 406 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER B 421 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE B 404 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ASP B 390 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL B 188 " --> pdb=" O ASP B 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 265 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA5, first strand: chain 'A' and resid 437 through 438 Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 500 removed outlier: 5.869A pdb=" N HIS B 311 " --> pdb=" O MET B 436 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLN B 438 " --> pdb=" O HIS B 311 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL B 313 " --> pdb=" O GLN B 438 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 263 through 265 282 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 2.04 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: 1888 1.33 - 1.45: 1429 1.45 - 1.57: 3629 1.57 - 1.69: 82 1.69 - 1.81: 56 Bond restraints: 7084 Sorted by residual: bond pdb=" C6 SSA B 601 " pdb=" N6 SSA B 601 " ideal model delta sigma weight residual 1.333 1.520 -0.187 2.00e-02 2.50e+03 8.77e+01 bond pdb=" C6 SSA A 601 " pdb=" N6 SSA A 601 " ideal model delta sigma weight residual 1.333 1.514 -0.181 2.00e-02 2.50e+03 8.18e+01 bond pdb=" O5' SSA B 601 " pdb=" S1 SSA B 601 " ideal model delta sigma weight residual 1.581 1.730 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" O2S SSA B 601 " pdb=" S1 SSA B 601 " ideal model delta sigma weight residual 1.435 1.583 -0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" O2S SSA A 601 " pdb=" S1 SSA A 601 " ideal model delta sigma weight residual 1.435 1.579 -0.144 2.00e-02 2.50e+03 5.17e+01 ... (remaining 7079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 9674 3.79 - 7.59: 86 7.59 - 11.38: 11 11.38 - 15.17: 0 15.17 - 18.97: 2 Bond angle restraints: 9773 Sorted by residual: angle pdb=" O1S SSA B 601 " pdb=" S1 SSA B 601 " pdb=" O2S SSA B 601 " ideal model delta sigma weight residual 121.34 102.37 18.97 3.00e+00 1.11e-01 4.00e+01 angle pdb=" O1S SSA A 601 " pdb=" S1 SSA A 601 " pdb=" O2S SSA A 601 " ideal model delta sigma weight residual 121.34 102.72 18.62 3.00e+00 1.11e-01 3.85e+01 angle pdb=" N1 SSA B 601 " pdb=" C6 SSA B 601 " pdb=" N6 SSA B 601 " ideal model delta sigma weight residual 119.38 108.60 10.78 3.00e+00 1.11e-01 1.29e+01 angle pdb=" N1 SSA A 601 " pdb=" C6 SSA A 601 " pdb=" N6 SSA A 601 " ideal model delta sigma weight residual 119.38 108.72 10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" N PHE B 386 " pdb=" CA PHE B 386 " pdb=" C PHE B 386 " ideal model delta sigma weight residual 109.24 114.98 -5.74 1.67e+00 3.59e-01 1.18e+01 ... (remaining 9768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.35: 4078 30.35 - 60.71: 206 60.71 - 91.06: 49 91.06 - 121.41: 1 121.41 - 151.76: 2 Dihedral angle restraints: 4336 sinusoidal: 2153 harmonic: 2183 Sorted by residual: dihedral pdb=" O4' U C 9 " pdb=" C1' U C 9 " pdb=" N1 U C 9 " pdb=" C2 U C 9 " ideal model delta sinusoidal sigma weight residual -160.00 -8.24 -151.76 1 1.50e+01 4.44e-03 8.03e+01 dihedral pdb=" O4' C C 8 " pdb=" C1' C C 8 " pdb=" N1 C C 8 " pdb=" C2 C C 8 " ideal model delta sinusoidal sigma weight residual -160.00 -10.36 -149.64 1 1.50e+01 4.44e-03 7.95e+01 dihedral pdb=" O4' A C 45 " pdb=" C1' A C 45 " pdb=" N9 A C 45 " pdb=" C4 A C 45 " ideal model delta sinusoidal sigma weight residual -106.00 -173.42 67.42 1 1.70e+01 3.46e-03 2.05e+01 ... (remaining 4333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1076 0.118 - 0.235: 31 0.235 - 0.353: 0 0.353 - 0.470: 0 0.470 - 0.588: 2 Chirality restraints: 1109 Sorted by residual: chirality pdb=" CA SSA B 601 " pdb=" CB SSA B 601 " pdb=" C9 SSA B 601 " pdb=" N10 SSA B 601 " both_signs ideal model delta sigma weight residual False -2.47 -3.06 0.59 2.00e-01 2.50e+01 8.64e+00 chirality pdb=" CA SSA A 601 " pdb=" CB SSA A 601 " pdb=" C9 SSA A 601 " pdb=" N10 SSA A 601 " both_signs ideal model delta sigma weight residual False -2.47 -3.03 0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" CA ARG A 227 " pdb=" N ARG A 227 " pdb=" C ARG A 227 " pdb=" CB ARG A 227 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.33e-01 ... (remaining 1106 not shown) Planarity restraints: 1139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 221 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C SER B 221 " 0.041 2.00e-02 2.50e+03 pdb=" O SER B 221 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS B 222 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 45 " -0.028 2.00e-02 2.50e+03 1.33e-02 4.87e+00 pdb=" N9 A C 45 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A C 45 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A C 45 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A C 45 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A C 45 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A C 45 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A C 45 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A C 45 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A C 45 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A C 45 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 347 " -0.014 2.00e-02 2.50e+03 1.50e-02 3.37e+00 pdb=" CG HIS B 347 " 0.032 2.00e-02 2.50e+03 pdb=" ND1 HIS B 347 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS B 347 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS B 347 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 347 " -0.003 2.00e-02 2.50e+03 ... (remaining 1136 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 49 2.51 - 3.11: 5218 3.11 - 3.71: 10911 3.71 - 4.30: 14874 4.30 - 4.90: 24178 Nonbonded interactions: 55230 Sorted by model distance: nonbonded pdb=" OH TYR A 329 " pdb=" OH TYR B 329 " model vdw 1.918 3.040 nonbonded pdb=" OG SSA A 601 " pdb=" O9 SSA A 601 " model vdw 2.005 3.040 nonbonded pdb=" OD1 ASN B 451 " pdb=" OG SSA B 601 " model vdw 2.019 3.040 nonbonded pdb=" OG SER A 224 " pdb=" OG SER A 228 " model vdw 2.020 3.040 nonbonded pdb=" O2' A C 45 " pdb=" O5' A C 46 " model vdw 2.039 3.040 ... (remaining 55225 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.650 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 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 : 0.010 0.187 7084 Z= 0.657 Angle : 1.045 18.967 9773 Z= 0.569 Chirality : 0.055 0.588 1109 Planarity : 0.004 0.045 1139 Dihedral : 18.068 151.765 2932 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.31 % Allowed : 12.66 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.04 (0.29), residues: 751 helix: 2.82 (0.29), residues: 296 sheet: 1.13 (0.54), residues: 87 loop : 0.23 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 409 HIS 0.016 0.002 HIS B 347 PHE 0.019 0.002 PHE B 404 TYR 0.019 0.003 TYR B 230 ARG 0.006 0.001 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 262 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8645 (mtt) cc_final: 0.8163 (ttm) REVERT: A 218 LYS cc_start: 0.4545 (mtmt) cc_final: 0.4302 (pttt) REVERT: A 226 HIS cc_start: 0.7146 (t70) cc_final: 0.6778 (t-90) REVERT: A 244 ASN cc_start: 0.8206 (m-40) cc_final: 0.7830 (t0) REVERT: A 248 ASN cc_start: 0.7613 (m-40) cc_final: 0.7394 (t0) REVERT: A 343 TYR cc_start: 0.6439 (t80) cc_final: 0.6216 (t80) REVERT: A 369 GLU cc_start: 0.8398 (tp30) cc_final: 0.8165 (mm-30) REVERT: A 370 GLU cc_start: 0.8711 (tt0) cc_final: 0.8411 (tm-30) REVERT: A 378 ILE cc_start: 0.7865 (mt) cc_final: 0.7592 (mm) REVERT: A 385 HIS cc_start: 0.5666 (t70) cc_final: 0.5208 (t70) REVERT: A 464 LEU cc_start: 0.7543 (mt) cc_final: 0.7160 (mt) REVERT: A 474 SER cc_start: 0.7368 (m) cc_final: 0.6596 (p) REVERT: B 99 LEU cc_start: 0.6943 (mt) cc_final: 0.6582 (mt) REVERT: B 290 ARG cc_start: 0.8667 (tpt90) cc_final: 0.8258 (mmm-85) REVERT: B 344 ARG cc_start: 0.6462 (mmt180) cc_final: 0.6168 (mmm-85) REVERT: B 363 GLN cc_start: 0.7819 (mp10) cc_final: 0.7457 (tt0) REVERT: B 435 ILE cc_start: 0.6856 (mt) cc_final: 0.6194 (mt) REVERT: B 501 ILE cc_start: 0.8156 (mm) cc_final: 0.7781 (mt) outliers start: 2 outliers final: 0 residues processed: 264 average time/residue: 0.2336 time to fit residues: 78.2201 Evaluate side-chains 138 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 45 optimal weight: 0.0870 chunk 70 optimal weight: 0.9990 overall best weight: 1.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 337 GLN A 375 GLN B 57 GLN B 102 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 7084 Z= 0.269 Angle : 0.691 8.902 9773 Z= 0.348 Chirality : 0.041 0.191 1109 Planarity : 0.006 0.088 1139 Dihedral : 17.453 152.384 1470 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.88 (0.30), residues: 751 helix: 2.49 (0.30), residues: 286 sheet: 1.48 (0.56), residues: 86 loop : 0.28 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 409 HIS 0.007 0.001 HIS B 347 PHE 0.022 0.002 PHE B 163 TYR 0.027 0.003 TYR B 47 ARG 0.005 0.001 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8352 (mtt) cc_final: 0.7965 (ttm) REVERT: A 218 LYS cc_start: 0.4403 (mtmt) cc_final: 0.4058 (pttt) REVERT: A 244 ASN cc_start: 0.8119 (m-40) cc_final: 0.7748 (t0) REVERT: A 332 GLU cc_start: 0.6194 (pm20) cc_final: 0.5808 (pm20) REVERT: A 426 THR cc_start: 0.7206 (p) cc_final: 0.6618 (p) REVERT: B 78 LYS cc_start: 0.7446 (tptt) cc_final: 0.6728 (mmtp) REVERT: B 185 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7072 (mp10) REVERT: B 210 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8356 (tt0) REVERT: B 250 LEU cc_start: 0.8752 (mm) cc_final: 0.8331 (mm) REVERT: B 317 ASP cc_start: 0.7940 (t0) cc_final: 0.7702 (t0) REVERT: B 340 ARG cc_start: 0.6792 (mmp-170) cc_final: 0.6264 (ttm170) REVERT: B 344 ARG cc_start: 0.6779 (mmt180) cc_final: 0.6336 (mmm-85) REVERT: B 353 MET cc_start: 0.6710 (mtm) cc_final: 0.5916 (mtm) REVERT: B 438 GLN cc_start: 0.7653 (pt0) cc_final: 0.6781 (pp30) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2097 time to fit residues: 50.1043 Evaluate side-chains 132 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN B 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7084 Z= 0.249 Angle : 0.661 8.162 9773 Z= 0.335 Chirality : 0.043 0.228 1109 Planarity : 0.005 0.051 1139 Dihedral : 17.266 151.554 1470 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.46 (0.30), residues: 751 helix: 2.23 (0.30), residues: 283 sheet: 0.74 (0.50), residues: 93 loop : 0.11 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 409 HIS 0.010 0.002 HIS A 385 PHE 0.015 0.002 PHE B 354 TYR 0.017 0.002 TYR B 45 ARG 0.005 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8343 (mtt) cc_final: 0.7992 (ttm) REVERT: A 211 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7857 (tptt) REVERT: A 244 ASN cc_start: 0.8149 (m-40) cc_final: 0.7705 (t0) REVERT: A 332 GLU cc_start: 0.6508 (pm20) cc_final: 0.6035 (pm20) REVERT: A 385 HIS cc_start: 0.5968 (t70) cc_final: 0.5485 (t70) REVERT: A 484 TYR cc_start: 0.6500 (m-80) cc_final: 0.6211 (m-80) REVERT: B 78 LYS cc_start: 0.7810 (tptt) cc_final: 0.7072 (mmtp) REVERT: B 185 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7287 (mp10) REVERT: B 274 MET cc_start: 0.7401 (mtt) cc_final: 0.6741 (mtm) REVERT: B 290 ARG cc_start: 0.8782 (tpt90) cc_final: 0.8526 (mmm-85) REVERT: B 291 PHE cc_start: 0.7470 (m-80) cc_final: 0.7241 (m-80) REVERT: B 340 ARG cc_start: 0.6875 (mmp-170) cc_final: 0.6307 (mtm180) REVERT: B 343 TYR cc_start: 0.6583 (t80) cc_final: 0.6361 (t80) REVERT: B 344 ARG cc_start: 0.7066 (mmt180) cc_final: 0.6829 (mmm160) REVERT: B 353 MET cc_start: 0.6626 (mtm) cc_final: 0.6255 (mtm) REVERT: B 361 LEU cc_start: 0.7939 (tp) cc_final: 0.7724 (tt) REVERT: B 391 MET cc_start: 0.7999 (mmp) cc_final: 0.7786 (tpp) REVERT: B 395 GLU cc_start: 0.6852 (tt0) cc_final: 0.6398 (tp30) REVERT: B 464 LEU cc_start: 0.6947 (mt) cc_final: 0.6711 (mt) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2161 time to fit residues: 47.6683 Evaluate side-chains 128 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN A 495 HIS B 217 GLN B 394 GLN B 438 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 7084 Z= 0.402 Angle : 0.783 7.943 9773 Z= 0.403 Chirality : 0.046 0.196 1109 Planarity : 0.007 0.088 1139 Dihedral : 17.777 158.647 1470 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.33 (0.29), residues: 751 helix: 1.31 (0.30), residues: 282 sheet: 0.16 (0.49), residues: 103 loop : -0.60 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 93 HIS 0.013 0.002 HIS B 347 PHE 0.031 0.003 PHE B 428 TYR 0.046 0.004 TYR B 47 ARG 0.010 0.001 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8423 (mtt) cc_final: 0.7950 (ttm) REVERT: A 244 ASN cc_start: 0.8363 (m-40) cc_final: 0.7851 (t0) REVERT: A 353 MET cc_start: 0.5669 (mtm) cc_final: 0.5383 (mtm) REVERT: A 367 LEU cc_start: 0.9225 (tp) cc_final: 0.8943 (tp) REVERT: A 385 HIS cc_start: 0.5886 (t70) cc_final: 0.5334 (t70) REVERT: A 391 MET cc_start: 0.7342 (mmm) cc_final: 0.7007 (mpp) REVERT: B 78 LYS cc_start: 0.8496 (tptt) cc_final: 0.7684 (mmtp) REVERT: B 164 TYR cc_start: 0.5974 (m-80) cc_final: 0.5700 (m-80) REVERT: B 224 SER cc_start: 0.9056 (p) cc_final: 0.8426 (t) REVERT: B 291 PHE cc_start: 0.7993 (m-80) cc_final: 0.7652 (m-80) REVERT: B 344 ARG cc_start: 0.7364 (mmt180) cc_final: 0.6982 (mmm160) REVERT: B 353 MET cc_start: 0.7048 (mtm) cc_final: 0.6659 (mtm) REVERT: B 391 MET cc_start: 0.7895 (mmp) cc_final: 0.7595 (mmt) REVERT: B 464 LEU cc_start: 0.7043 (mt) cc_final: 0.6835 (mt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2192 time to fit residues: 42.7115 Evaluate side-chains 103 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7084 Z= 0.223 Angle : 0.639 7.313 9773 Z= 0.322 Chirality : 0.041 0.194 1109 Planarity : 0.005 0.047 1139 Dihedral : 17.479 158.772 1470 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.61 (0.30), residues: 751 helix: 1.67 (0.31), residues: 282 sheet: 0.03 (0.49), residues: 103 loop : -0.46 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 93 HIS 0.007 0.001 HIS B 385 PHE 0.025 0.002 PHE B 354 TYR 0.020 0.002 TYR B 47 ARG 0.007 0.001 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8374 (mtt) cc_final: 0.7909 (ttm) REVERT: A 218 LYS cc_start: 0.4817 (mtmt) cc_final: 0.4455 (mtmt) REVERT: A 244 ASN cc_start: 0.8200 (m-40) cc_final: 0.7845 (t0) REVERT: A 367 LEU cc_start: 0.9098 (tp) cc_final: 0.8835 (tp) REVERT: A 378 ILE cc_start: 0.7746 (mt) cc_final: 0.7517 (mm) REVERT: A 385 HIS cc_start: 0.5702 (t70) cc_final: 0.5358 (t70) REVERT: B 78 LYS cc_start: 0.8660 (tptt) cc_final: 0.7789 (mmtp) REVERT: B 80 GLU cc_start: 0.6307 (tp30) cc_final: 0.5461 (mt-10) REVERT: B 224 SER cc_start: 0.9128 (p) cc_final: 0.8759 (p) REVERT: B 250 LEU cc_start: 0.8505 (mm) cc_final: 0.8268 (mm) REVERT: B 291 PHE cc_start: 0.8095 (m-80) cc_final: 0.7746 (m-80) REVERT: B 344 ARG cc_start: 0.7111 (mmt180) cc_final: 0.6727 (mmm160) REVERT: B 363 GLN cc_start: 0.7583 (mp10) cc_final: 0.7358 (tt0) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1843 time to fit residues: 35.4217 Evaluate side-chains 109 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.6922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7084 Z= 0.376 Angle : 0.730 6.744 9773 Z= 0.370 Chirality : 0.044 0.189 1109 Planarity : 0.005 0.049 1139 Dihedral : 17.743 161.734 1470 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.07 (0.30), residues: 751 helix: 1.38 (0.30), residues: 283 sheet: -0.18 (0.48), residues: 105 loop : -0.96 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 409 HIS 0.011 0.002 HIS B 347 PHE 0.019 0.003 PHE B 354 TYR 0.022 0.003 TYR B 47 ARG 0.012 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8410 (mtt) cc_final: 0.7845 (ttm) REVERT: A 218 LYS cc_start: 0.4786 (mtmt) cc_final: 0.4429 (mtmt) REVERT: A 367 LEU cc_start: 0.9277 (tp) cc_final: 0.9011 (tp) REVERT: A 378 ILE cc_start: 0.7476 (mt) cc_final: 0.7249 (mm) REVERT: A 385 HIS cc_start: 0.5618 (t70) cc_final: 0.5172 (t70) REVERT: A 391 MET cc_start: 0.7520 (mmm) cc_final: 0.7275 (mpp) REVERT: B 59 ASP cc_start: 0.6653 (t0) cc_final: 0.6324 (t0) REVERT: B 78 LYS cc_start: 0.8718 (tptt) cc_final: 0.7869 (mmtp) REVERT: B 80 GLU cc_start: 0.5974 (tp30) cc_final: 0.5188 (mt-10) REVERT: B 224 SER cc_start: 0.9166 (p) cc_final: 0.8820 (p) REVERT: B 291 PHE cc_start: 0.8220 (m-80) cc_final: 0.7780 (m-80) REVERT: B 344 ARG cc_start: 0.7328 (mmt180) cc_final: 0.6852 (mmm160) REVERT: B 353 MET cc_start: 0.7041 (mtm) cc_final: 0.6816 (mtm) REVERT: B 418 GLU cc_start: 0.5527 (tt0) cc_final: 0.5289 (tt0) REVERT: B 428 PHE cc_start: 0.7994 (t80) cc_final: 0.7780 (t80) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1740 time to fit residues: 30.4566 Evaluate side-chains 102 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0870 chunk 42 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 0.0040 chunk 47 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.4970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.7003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7084 Z= 0.185 Angle : 0.632 6.331 9773 Z= 0.316 Chirality : 0.041 0.218 1109 Planarity : 0.004 0.040 1139 Dihedral : 17.495 160.499 1470 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.55 (0.30), residues: 751 helix: 1.84 (0.31), residues: 278 sheet: -0.12 (0.48), residues: 108 loop : -0.63 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 93 HIS 0.005 0.001 HIS A 222 PHE 0.021 0.001 PHE B 354 TYR 0.017 0.002 TYR B 164 ARG 0.007 0.001 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.692 Fit side-chains REVERT: A 191 MET cc_start: 0.8396 (mtt) cc_final: 0.7915 (ttm) REVERT: A 244 ASN cc_start: 0.8286 (m-40) cc_final: 0.7674 (t0) REVERT: A 367 LEU cc_start: 0.9123 (tp) cc_final: 0.8805 (tp) REVERT: A 378 ILE cc_start: 0.7647 (mt) cc_final: 0.7379 (mm) REVERT: A 385 HIS cc_start: 0.5531 (t70) cc_final: 0.5239 (t70) REVERT: A 428 PHE cc_start: 0.8338 (t80) cc_final: 0.8093 (t80) REVERT: B 78 LYS cc_start: 0.8692 (tptt) cc_final: 0.7810 (mmtp) REVERT: B 80 GLU cc_start: 0.6121 (tp30) cc_final: 0.5258 (mt-10) REVERT: B 291 PHE cc_start: 0.8101 (m-80) cc_final: 0.7724 (m-80) REVERT: B 343 TYR cc_start: 0.6795 (t80) cc_final: 0.6453 (t80) REVERT: B 344 ARG cc_start: 0.7238 (mmt180) cc_final: 0.6807 (mmm160) REVERT: B 353 MET cc_start: 0.6864 (mtm) cc_final: 0.6660 (mtm) REVERT: B 418 GLU cc_start: 0.5177 (tt0) cc_final: 0.4951 (tt0) REVERT: B 428 PHE cc_start: 0.7652 (t80) cc_final: 0.7295 (t80) REVERT: B 432 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7566 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2007 time to fit residues: 35.6618 Evaluate side-chains 101 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS ** A 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN B 438 GLN ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.7387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 7084 Z= 0.414 Angle : 0.758 9.087 9773 Z= 0.381 Chirality : 0.045 0.225 1109 Planarity : 0.006 0.042 1139 Dihedral : 17.842 162.460 1470 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.04 (0.30), residues: 751 helix: 1.39 (0.31), residues: 284 sheet: -0.51 (0.48), residues: 105 loop : -1.02 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 409 HIS 0.010 0.002 HIS B 347 PHE 0.019 0.003 PHE B 354 TYR 0.023 0.003 TYR B 230 ARG 0.009 0.001 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.8411 (mtt) cc_final: 0.7908 (ttm) REVERT: A 244 ASN cc_start: 0.8548 (m-40) cc_final: 0.7818 (t0) REVERT: A 367 LEU cc_start: 0.9136 (tp) cc_final: 0.8895 (tp) REVERT: A 385 HIS cc_start: 0.5581 (t70) cc_final: 0.5170 (t70) REVERT: A 390 ASP cc_start: 0.7025 (t0) cc_final: 0.6577 (t0) REVERT: B 78 LYS cc_start: 0.8736 (tptt) cc_final: 0.7903 (mmtp) REVERT: B 80 GLU cc_start: 0.6478 (tp30) cc_final: 0.5626 (mt-10) REVERT: B 210 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7893 (mm-30) REVERT: B 291 PHE cc_start: 0.8252 (m-80) cc_final: 0.7851 (m-80) REVERT: B 344 ARG cc_start: 0.7375 (mmt180) cc_final: 0.6925 (mmm160) REVERT: B 353 MET cc_start: 0.7014 (mtm) cc_final: 0.6784 (mtm) REVERT: B 418 GLU cc_start: 0.5574 (tt0) cc_final: 0.5216 (tt0) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1875 time to fit residues: 28.5066 Evaluate side-chains 93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 240 HIS B 394 GLN ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.7442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7084 Z= 0.194 Angle : 0.640 7.382 9773 Z= 0.320 Chirality : 0.041 0.187 1109 Planarity : 0.004 0.036 1139 Dihedral : 17.615 161.140 1470 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.38 (0.30), residues: 751 helix: 1.89 (0.31), residues: 278 sheet: -0.56 (0.47), residues: 105 loop : -0.78 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 93 HIS 0.006 0.001 HIS B 347 PHE 0.025 0.002 PHE A 428 TYR 0.017 0.002 TYR B 164 ARG 0.006 0.001 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.690 Fit side-chains REVERT: A 191 MET cc_start: 0.8322 (mtt) cc_final: 0.7838 (ttm) REVERT: A 244 ASN cc_start: 0.8306 (m-40) cc_final: 0.7632 (t0) REVERT: A 367 LEU cc_start: 0.9064 (tp) cc_final: 0.8751 (tp) REVERT: A 385 HIS cc_start: 0.5297 (t70) cc_final: 0.5047 (t70) REVERT: B 78 LYS cc_start: 0.8793 (tptt) cc_final: 0.7929 (mmtp) REVERT: B 80 GLU cc_start: 0.6274 (tp30) cc_final: 0.5412 (mt-10) REVERT: B 210 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7837 (mm-30) REVERT: B 291 PHE cc_start: 0.8262 (m-80) cc_final: 0.7717 (m-80) REVERT: B 344 ARG cc_start: 0.7331 (mmt180) cc_final: 0.6878 (mmm160) REVERT: B 418 GLU cc_start: 0.5207 (tt0) cc_final: 0.4930 (tt0) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1919 time to fit residues: 34.6391 Evaluate side-chains 103 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 18 optimal weight: 0.0980 chunk 57 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 HIS B 394 GLN ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.7673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7084 Z= 0.326 Angle : 0.727 8.049 9773 Z= 0.367 Chirality : 0.044 0.193 1109 Planarity : 0.005 0.035 1139 Dihedral : 17.828 160.725 1470 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.05 (0.30), residues: 751 helix: 1.59 (0.31), residues: 284 sheet: -0.73 (0.46), residues: 105 loop : -1.00 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 409 HIS 0.009 0.001 HIS B 347 PHE 0.034 0.002 PHE B 386 TYR 0.023 0.003 TYR B 164 ARG 0.010 0.001 ARG B 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.8401 (mtt) cc_final: 0.7891 (ttm) REVERT: A 244 ASN cc_start: 0.8421 (m-40) cc_final: 0.7747 (t0) REVERT: A 367 LEU cc_start: 0.9114 (tp) cc_final: 0.8768 (tp) REVERT: A 385 HIS cc_start: 0.5400 (t70) cc_final: 0.5052 (t70) REVERT: B 78 LYS cc_start: 0.8735 (tptt) cc_final: 0.7908 (mmtp) REVERT: B 80 GLU cc_start: 0.6276 (tp30) cc_final: 0.5427 (mt-10) REVERT: B 210 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7900 (mm-30) REVERT: B 291 PHE cc_start: 0.8148 (m-80) cc_final: 0.7771 (m-80) REVERT: B 344 ARG cc_start: 0.7372 (mmt180) cc_final: 0.6936 (mmm160) REVERT: B 407 GLU cc_start: 0.8563 (tt0) cc_final: 0.8244 (tt0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2065 time to fit residues: 32.0572 Evaluate side-chains 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.171358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.143218 restraints weight = 9618.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.146793 restraints weight = 6015.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.149216 restraints weight = 4224.375| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.7818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7084 Z= 0.248 Angle : 0.672 6.366 9773 Z= 0.339 Chirality : 0.042 0.190 1109 Planarity : 0.005 0.036 1139 Dihedral : 17.769 159.535 1470 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.15 (0.30), residues: 751 helix: 1.74 (0.31), residues: 284 sheet: -0.71 (0.48), residues: 97 loop : -0.98 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 409 HIS 0.007 0.001 HIS B 347 PHE 0.022 0.002 PHE B 354 TYR 0.023 0.002 TYR B 164 ARG 0.007 0.001 ARG B 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1572.01 seconds wall clock time: 33 minutes 32.59 seconds (2012.59 seconds total)