Starting phenix.real_space_refine on Wed Mar 12 04:06:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u2a_26310/03_2025/7u2a_26310.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u2a_26310/03_2025/7u2a_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_26310/03_2025/7u2a_26310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u2a_26310/03_2025/7u2a_26310.map" model { file = "/net/cci-nas-00/data/ceres_data/7u2a_26310/03_2025/7u2a_26310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u2a_26310/03_2025/7u2a_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.82, 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: 2.11 Conformation dependent library (CDL) restraints added in 701.1 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: 2.51 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: 2.61 Time building geometry restraints manager: 2.45 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: 0.010 Normalize map: mean=0, sd=1: 0.450 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.160 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.280 ------------------------------------------------------------------------------- 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 : 0.693 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: 0.2238 time to fit residues: 75.2471 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 : 0.719 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.189025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.162823 restraints weight = 9123.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.166837 restraints weight = 5306.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.169565 restraints weight = 3529.489| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.3441 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 8.895 9773 Z= 0.349 Chirality : 0.041 0.191 1109 Planarity : 0.006 0.089 1139 Dihedral : 17.456 152.399 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 0.006 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 : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.4908 (mtmt) cc_final: 0.4425 (pttt) REVERT: A 332 GLU cc_start: 0.6684 (pm20) cc_final: 0.6324 (pm20) REVERT: B 78 LYS cc_start: 0.7793 (tptt) cc_final: 0.7050 (mmtp) REVERT: B 185 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7372 (mp10) REVERT: B 210 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7446 (tt0) REVERT: B 250 LEU cc_start: 0.8489 (mm) cc_final: 0.7954 (mm) REVERT: B 353 MET cc_start: 0.5909 (mtm) cc_final: 0.5295 (mtm) REVERT: B 438 GLN cc_start: 0.7346 (pt0) cc_final: 0.6925 (pp30) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1995 time to fit residues: 47.3034 Evaluate side-chains 129 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 363 GLN A 495 HIS B 438 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.183462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.156124 restraints weight = 9299.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.160067 restraints weight = 5530.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.162771 restraints weight = 3756.367| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7084 Z= 0.270 Angle : 0.674 8.617 9773 Z= 0.342 Chirality : 0.043 0.202 1109 Planarity : 0.005 0.048 1139 Dihedral : 17.282 151.963 1470 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % 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: 1.42 (0.30), residues: 751 helix: 2.18 (0.30), residues: 283 sheet: 0.83 (0.52), residues: 88 loop : 0.08 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 409 HIS 0.010 0.002 HIS A 226 PHE 0.017 0.002 PHE B 354 TYR 0.018 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 169 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 GLU cc_start: 0.6762 (pm20) cc_final: 0.6537 (pm20) REVERT: A 340 ARG cc_start: 0.7516 (mtm110) cc_final: 0.7069 (mtm110) REVERT: A 385 HIS cc_start: 0.6301 (t70) cc_final: 0.5923 (t70) REVERT: A 428 PHE cc_start: 0.8117 (t80) cc_final: 0.7795 (t80) REVERT: B 78 LYS cc_start: 0.8077 (tptt) cc_final: 0.7270 (mmtp) REVERT: B 274 MET cc_start: 0.7035 (mtt) cc_final: 0.6549 (mtm) REVERT: B 290 ARG cc_start: 0.8544 (tpt90) cc_final: 0.8153 (mmm-85) REVERT: B 353 MET cc_start: 0.5927 (mtm) cc_final: 0.5704 (mtm) REVERT: B 361 LEU cc_start: 0.7944 (tp) cc_final: 0.7557 (tt) REVERT: B 432 ARG cc_start: 0.7223 (mmt180) cc_final: 0.6983 (mtt-85) REVERT: B 464 LEU cc_start: 0.6867 (mt) cc_final: 0.6599 (mt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2156 time to fit residues: 47.4004 Evaluate side-chains 120 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 0.0570 chunk 57 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- 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** B 394 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.184483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.156521 restraints weight = 9315.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.160148 restraints weight = 5603.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.162939 restraints weight = 3865.283| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7084 Z= 0.205 Angle : 0.610 6.646 9773 Z= 0.309 Chirality : 0.041 0.192 1109 Planarity : 0.005 0.071 1139 Dihedral : 17.268 151.935 1470 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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: 1.23 (0.30), residues: 751 helix: 2.19 (0.30), residues: 282 sheet: 0.32 (0.48), residues: 105 loop : -0.08 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 93 HIS 0.007 0.001 HIS B 347 PHE 0.018 0.002 PHE B 63 TYR 0.020 0.002 TYR B 500 ARG 0.007 0.001 ARG B 431 *********************** 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 160 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.5358 (mtmt) cc_final: 0.4695 (pttt) REVERT: A 274 MET cc_start: 0.3964 (mtp) cc_final: 0.3659 (mtt) REVERT: A 340 ARG cc_start: 0.7566 (mtm110) cc_final: 0.7123 (mtm110) REVERT: A 385 HIS cc_start: 0.6256 (t70) cc_final: 0.5887 (t70) REVERT: A 410 MET cc_start: 0.4785 (mtt) cc_final: 0.3496 (mtp) REVERT: A 428 PHE cc_start: 0.8179 (t80) cc_final: 0.7820 (t80) REVERT: A 499 GLN cc_start: 0.6397 (mt0) cc_final: 0.6123 (mt0) REVERT: B 78 LYS cc_start: 0.8092 (tptt) cc_final: 0.7420 (mmtp) REVERT: B 210 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7328 (tt0) REVERT: B 274 MET cc_start: 0.7130 (mtt) cc_final: 0.6895 (mtm) REVERT: B 290 ARG cc_start: 0.8631 (tpt90) cc_final: 0.8171 (mmm-85) REVERT: B 432 ARG cc_start: 0.7273 (mmt180) cc_final: 0.6983 (ttt180) REVERT: B 464 LEU cc_start: 0.6875 (mt) cc_final: 0.6664 (mt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1953 time to fit residues: 41.2729 Evaluate side-chains 117 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 HIS B 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.173210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.144944 restraints weight = 9483.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.148444 restraints weight = 5881.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.150852 restraints weight = 4176.247| |-----------------------------------------------------------------------------| r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.6002 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= 0.383 Angle : 0.734 7.915 9773 Z= 0.375 Chirality : 0.045 0.192 1109 Planarity : 0.006 0.051 1139 Dihedral : 17.505 156.639 1470 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: 0.70 (0.30), residues: 751 helix: 1.83 (0.31), residues: 282 sheet: 0.06 (0.49), residues: 103 loop : -0.48 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 409 HIS 0.011 0.002 HIS B 347 PHE 0.017 0.003 PHE B 404 TYR 0.037 0.003 TYR B 47 ARG 0.007 0.001 ARG A 216 *********************** 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 147 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7277 (mpp80) cc_final: 0.6913 (mpp80) REVERT: A 340 ARG cc_start: 0.7739 (mtm110) cc_final: 0.7342 (mtm110) REVERT: A 376 MET cc_start: 0.7923 (mtp) cc_final: 0.7647 (mtp) REVERT: A 385 HIS cc_start: 0.6316 (t70) cc_final: 0.5935 (t70) REVERT: A 501 ILE cc_start: 0.7164 (pt) cc_final: 0.6693 (mt) REVERT: B 78 LYS cc_start: 0.8627 (tptt) cc_final: 0.7784 (mmtp) REVERT: B 210 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7385 (tt0) REVERT: B 353 MET cc_start: 0.6505 (mtm) cc_final: 0.6207 (mtm) REVERT: B 428 PHE cc_start: 0.7971 (t80) cc_final: 0.7720 (t80) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2228 time to fit residues: 42.3545 Evaluate side-chains 105 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 5 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 GLN B 311 HIS B 394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.175852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.147474 restraints weight = 9553.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.151085 restraints weight = 5887.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.153656 restraints weight = 4135.668| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7084 Z= 0.232 Angle : 0.634 6.673 9773 Z= 0.319 Chirality : 0.041 0.194 1109 Planarity : 0.004 0.045 1139 Dihedral : 17.398 156.287 1470 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: 0.78 (0.30), residues: 751 helix: 1.97 (0.31), residues: 282 sheet: 0.06 (0.49), residues: 102 loop : -0.49 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 93 HIS 0.008 0.001 HIS B 347 PHE 0.027 0.002 PHE B 354 TYR 0.022 0.002 TYR B 47 ARG 0.009 0.001 ARG B 77 *********************** 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 137 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.5566 (mtmt) cc_final: 0.5162 (mtmt) REVERT: A 376 MET cc_start: 0.7881 (mtp) cc_final: 0.7598 (mtp) REVERT: A 501 ILE cc_start: 0.7180 (pt) cc_final: 0.6774 (mt) REVERT: B 78 LYS cc_start: 0.8650 (tptt) cc_final: 0.7842 (mmtp) REVERT: B 210 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7349 (tt0) REVERT: B 301 GLU cc_start: 0.7676 (pp20) cc_final: 0.7426 (pp20) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1681 time to fit residues: 31.4396 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 : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 0.9990 chunk 67 optimal weight: 0.0870 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 42 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.180663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.152886 restraints weight = 9431.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.156649 restraints weight = 5739.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.159236 restraints weight = 3988.257| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.6538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7084 Z= 0.182 Angle : 0.609 7.038 9773 Z= 0.304 Chirality : 0.040 0.165 1109 Planarity : 0.004 0.044 1139 Dihedral : 17.268 153.949 1470 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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: 0.85 (0.31), residues: 751 helix: 2.09 (0.31), residues: 284 sheet: -0.10 (0.48), residues: 108 loop : -0.44 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 93 HIS 0.006 0.001 HIS B 347 PHE 0.024 0.001 PHE B 354 TYR 0.015 0.002 TYR B 47 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 133 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.744 Fit side-chains REVERT: A 218 LYS cc_start: 0.5514 (mtmt) cc_final: 0.5274 (mtmt) REVERT: A 376 MET cc_start: 0.7710 (mtp) cc_final: 0.7503 (mtp) REVERT: B 78 LYS cc_start: 0.8640 (tptt) cc_final: 0.7967 (mmtp) REVERT: B 274 MET cc_start: 0.6376 (mtp) cc_final: 0.6014 (mtm) REVERT: B 428 PHE cc_start: 0.7518 (t80) cc_final: 0.6706 (t80) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1582 time to fit residues: 29.2835 Evaluate side-chains 97 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 39 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.177569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.149169 restraints weight = 9611.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.152803 restraints weight = 5955.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.155344 restraints weight = 4199.615| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.6729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7084 Z= 0.241 Angle : 0.645 8.950 9773 Z= 0.324 Chirality : 0.041 0.182 1109 Planarity : 0.005 0.047 1139 Dihedral : 17.339 153.711 1470 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % 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: 0.66 (0.31), residues: 751 helix: 2.05 (0.31), residues: 284 sheet: -0.33 (0.48), residues: 108 loop : -0.61 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 409 HIS 0.008 0.001 HIS B 347 PHE 0.022 0.002 PHE B 428 TYR 0.017 0.002 TYR B 47 ARG 0.006 0.001 ARG B 143 *********************** 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 122 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 218 LYS cc_start: 0.5407 (mtmt) cc_final: 0.5152 (mtmt) REVERT: A 376 MET cc_start: 0.7834 (mtp) cc_final: 0.7532 (mtp) REVERT: B 78 LYS cc_start: 0.8682 (tptt) cc_final: 0.7998 (mmtp) REVERT: B 274 MET cc_start: 0.6448 (mtp) cc_final: 0.6146 (mtm) REVERT: B 290 ARG cc_start: 0.8215 (tpt90) cc_final: 0.7912 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1726 time to fit residues: 29.0360 Evaluate side-chains 96 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 75 optimal weight: 0.0010 chunk 9 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.182025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.153804 restraints weight = 9458.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.157656 restraints weight = 5691.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.160293 restraints weight = 3896.966| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.6913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7084 Z= 0.183 Angle : 0.607 6.279 9773 Z= 0.305 Chirality : 0.040 0.227 1109 Planarity : 0.005 0.056 1139 Dihedral : 17.342 151.754 1470 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: 0.63 (0.31), residues: 751 helix: 2.02 (0.31), residues: 284 sheet: -0.55 (0.46), residues: 110 loop : -0.55 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 93 HIS 0.006 0.001 HIS B 347 PHE 0.024 0.002 PHE B 354 TYR 0.012 0.001 TYR B 47 ARG 0.011 0.001 ARG B 77 *********************** 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 124 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 LYS cc_start: 0.5389 (mtmt) cc_final: 0.5157 (mtmt) REVERT: A 367 LEU cc_start: 0.9002 (tp) cc_final: 0.8626 (tp) REVERT: A 392 PRO cc_start: 0.7668 (Cg_endo) cc_final: 0.7361 (Cg_exo) REVERT: B 78 LYS cc_start: 0.8837 (tptt) cc_final: 0.8117 (mmtp) REVERT: B 80 GLU cc_start: 0.6119 (tp30) cc_final: 0.5645 (mt-10) REVERT: B 274 MET cc_start: 0.6404 (mtp) cc_final: 0.6098 (mtm) REVERT: B 290 ARG cc_start: 0.8601 (tpt90) cc_final: 0.8293 (mmm-85) REVERT: B 436 MET cc_start: 0.7520 (mpp) cc_final: 0.7247 (mmt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1786 time to fit residues: 30.2217 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 : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 56 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.0020 chunk 3 optimal weight: 0.0770 chunk 28 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.179159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.150617 restraints weight = 9738.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.154426 restraints weight = 5953.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.157064 restraints weight = 4144.509| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.7110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7084 Z= 0.219 Angle : 0.630 6.499 9773 Z= 0.316 Chirality : 0.041 0.210 1109 Planarity : 0.005 0.048 1139 Dihedral : 17.240 150.963 1470 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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 (0.31), residues: 751 helix: 2.02 (0.31), residues: 284 sheet: -0.66 (0.46), residues: 110 loop : -0.55 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 409 HIS 0.007 0.001 HIS B 347 PHE 0.023 0.002 PHE B 354 TYR 0.014 0.002 TYR B 47 ARG 0.006 0.001 ARG A 340 ********************** 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 118 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6630 (mmm) cc_final: 0.5917 (mmt) REVERT: A 337 GLN cc_start: 0.6279 (pm20) cc_final: 0.5428 (mp10) REVERT: A 340 ARG cc_start: 0.7412 (mtm110) cc_final: 0.7131 (ptp-110) REVERT: A 392 PRO cc_start: 0.7864 (Cg_endo) cc_final: 0.7546 (Cg_exo) REVERT: B 78 LYS cc_start: 0.8861 (tptt) cc_final: 0.8179 (mmtp) REVERT: B 80 GLU cc_start: 0.6202 (tp30) cc_final: 0.5801 (mt-10) REVERT: B 274 MET cc_start: 0.6301 (mtp) cc_final: 0.6040 (mtm) REVERT: B 361 LEU cc_start: 0.8167 (tp) cc_final: 0.7819 (tt) REVERT: B 436 MET cc_start: 0.7471 (mpp) cc_final: 0.7242 (mmt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1517 time to fit residues: 25.3790 Evaluate side-chains 95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 55 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 75 optimal weight: 0.0070 chunk 15 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.182752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.154919 restraints weight = 9460.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.158849 restraints weight = 5709.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.161390 restraints weight = 3915.748| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.7273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7084 Z= 0.182 Angle : 0.614 7.420 9773 Z= 0.307 Chirality : 0.040 0.185 1109 Planarity : 0.004 0.046 1139 Dihedral : 17.119 148.862 1470 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: 0.54 (0.31), residues: 751 helix: 1.94 (0.31), residues: 285 sheet: -0.75 (0.46), residues: 110 loop : -0.54 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 409 HIS 0.005 0.001 HIS B 347 PHE 0.025 0.002 PHE A 371 TYR 0.010 0.001 TYR B 45 ARG 0.006 0.001 ARG A 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2188.53 seconds wall clock time: 38 minutes 56.63 seconds (2336.63 seconds total)