Starting phenix.real_space_refine on Wed Mar 12 11:49:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ffy_29070/03_2025/8ffy_29070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ffy_29070/03_2025/8ffy_29070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ffy_29070/03_2025/8ffy_29070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ffy_29070/03_2025/8ffy_29070.map" model { file = "/net/cci-nas-00/data/ceres_data/8ffy_29070/03_2025/8ffy_29070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ffy_29070/03_2025/8ffy_29070.cif" } resolution = 3.6 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= 0.011 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 61 5.49 5 S 34 5.16 5 C 4455 2.51 5 N 1333 2.21 5 O 1559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 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: 7442 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2493 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3590 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 424} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1301 Classifications: {'RNA': 61} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 6, 'rna3p_pur': 29, 'rna3p_pyr': 25} Link IDs: {'rna2p': 6, 'rna3p': 54} Chain breaks: 1 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: 6.33, per 1000 atoms: 0.85 Number of scatterers: 7442 At special positions: 0 Unit cell: (105.8, 80.5, 113.85, 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 61 15.00 O 1559 8.00 N 1333 7.00 C 4455 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: 5.43 Conformation dependent library (CDL) restraints added in 714.1 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1422 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 40.9% alpha, 17.3% beta 20 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 2.97 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 245 removed outlier: 3.510A pdb=" N LEU A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 254 Processing helix chain 'A' and resid 266 through 273 Processing helix chain 'A' and resid 299 through 307 removed outlier: 4.054A pdb=" N GLY A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 383 Processing helix chain 'A' and resid 427 through 434 Processing helix chain 'A' and resid 457 through 468 Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'B' and resid 42 through 51 Processing helix chain 'B' and resid 59 through 65 removed outlier: 4.155A pdb=" N PHE B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 78 removed outlier: 3.536A pdb=" N ALA B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 121 Processing helix chain 'B' and resid 132 through 168 Proline residue: B 154 - end of helix Processing helix chain 'B' and resid 204 through 212 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'B' and resid 265 through 273 removed outlier: 3.800A pdb=" N PHE B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 309 removed outlier: 3.780A 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 427 through 434 Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 481 through 486 Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 192 removed outlier: 7.069A pdb=" N VAL A 388 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N MET A 191 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N PHE A 386 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG A 402 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER A 423 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 404 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER A 421 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 406 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N VAL A 419 " --> pdb=" O CYS A 455 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N CYS A 455 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N SER A 421 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 453 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS A 425 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 449 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS A 448 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 351 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ALA A 456 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR A 349 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 231 through 232 removed outlier: 3.618A pdb=" N LEU A 231 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER B 325 " --> pdb=" O MET B 258 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N THR B 349 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA B 456 " --> pdb=" O THR B 349 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 351 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 357 " --> pdb=" O HIS B 448 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS B 448 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER B 421 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N CYS B 455 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 9.504A pdb=" N VAL B 419 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE B 416 " --> pdb=" O MET B 410 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N MET B 410 " --> pdb=" O PHE B 416 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU B 418 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA B 408 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 420 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 402 " --> pdb=" O ASN B 424 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS B 190 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP B 390 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL B 188 " --> pdb=" O ASP B 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 265 Processing sheet with id=AA5, first strand: chain 'A' and resid 444 through 446 removed outlier: 5.642A pdb=" N HIS A 311 " --> pdb=" O MET A 436 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLN A 438 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 313 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 475 through 476 removed outlier: 3.565A pdb=" N VAL A 475 " --> pdb=" O ILE A 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 263 through 264 Processing sheet with id=AA8, first strand: chain 'B' and resid 436 through 438 Processing sheet with id=AA9, first strand: chain 'B' and resid 475 through 476 288 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 2.91 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2124 1.34 - 1.45: 1565 1.45 - 1.57: 3860 1.57 - 1.69: 128 1.69 - 1.81: 56 Bond restraints: 7733 Sorted by residual: bond pdb=" C6 SSA A 601 " pdb=" N6 SSA A 601 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.13e+01 bond pdb=" C6 SSA B 601 " pdb=" N6 SSA B 601 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.09e+01 bond pdb=" O5' SSA B 601 " pdb=" S1 SSA B 601 " ideal model delta sigma weight residual 1.581 1.735 -0.154 2.00e-02 2.50e+03 5.89e+01 bond pdb=" O5' SSA A 601 " pdb=" S1 SSA A 601 " ideal model delta sigma weight residual 1.581 1.733 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" O2S SSA A 601 " pdb=" S1 SSA A 601 " ideal model delta sigma weight residual 1.435 1.586 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 7728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 10721 4.04 - 8.08: 36 8.08 - 12.11: 11 12.11 - 16.15: 0 16.15 - 20.19: 2 Bond angle restraints: 10770 Sorted by residual: angle pdb=" C3' U C 72 " pdb=" O3' U C 72 " pdb=" P G C 73 " ideal model delta sigma weight residual 120.20 109.80 10.40 1.50e+00 4.44e-01 4.80e+01 angle pdb=" O1S SSA B 601 " pdb=" S1 SSA B 601 " pdb=" O2S SSA B 601 " ideal model delta sigma weight residual 121.34 101.15 20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" O1S SSA A 601 " pdb=" S1 SSA A 601 " pdb=" O2S SSA A 601 " ideal model delta sigma weight residual 121.34 101.15 20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" C3' U C 71 " pdb=" O3' U C 71 " pdb=" P U C 72 " ideal model delta sigma weight residual 120.20 111.06 9.14 1.50e+00 4.44e-01 3.71e+01 angle pdb=" C HIS A 226 " pdb=" N ARG A 227 " pdb=" CA ARG A 227 " ideal model delta sigma weight residual 122.93 113.99 8.94 1.51e+00 4.39e-01 3.51e+01 ... (remaining 10765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.51: 4495 32.51 - 65.02: 267 65.02 - 97.54: 37 97.54 - 130.05: 0 130.05 - 162.56: 1 Dihedral angle restraints: 4800 sinusoidal: 2589 harmonic: 2211 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 232.00 162.24 69.76 1 1.70e+01 3.46e-03 2.17e+01 dihedral pdb=" C5' U C 9 " pdb=" C4' U C 9 " pdb=" C3' U C 9 " pdb=" O3' U C 9 " ideal model delta sinusoidal sigma weight residual 147.00 116.13 30.87 1 8.00e+00 1.56e-02 2.12e+01 dihedral pdb=" C3' U C 9 " pdb=" C4' U C 9 " pdb=" O4' U C 9 " pdb=" C1' U C 9 " ideal model delta sinusoidal sigma weight residual -2.00 24.84 -26.84 1 8.00e+00 1.56e-02 1.62e+01 ... (remaining 4797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1193 0.110 - 0.220: 36 0.220 - 0.329: 0 0.329 - 0.439: 3 0.439 - 0.549: 3 Chirality restraints: 1235 Sorted by residual: 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 -3.02 0.55 2.00e-01 2.50e+01 7.53e+00 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 -3.01 0.55 2.00e-01 2.50e+01 7.43e+00 chirality pdb=" P U C 71 " pdb=" OP1 U C 71 " pdb=" OP2 U C 71 " pdb=" O5' U C 71 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.54e+00 ... (remaining 1232 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 226 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C HIS A 226 " -0.038 2.00e-02 2.50e+03 pdb=" O HIS A 226 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG A 227 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U C 71 " -0.012 2.00e-02 2.50e+03 1.25e-02 3.50e+00 pdb=" N1 U C 71 " 0.018 2.00e-02 2.50e+03 pdb=" C2 U C 71 " 0.020 2.00e-02 2.50e+03 pdb=" O2 U C 71 " -0.006 2.00e-02 2.50e+03 pdb=" N3 U C 71 " -0.011 2.00e-02 2.50e+03 pdb=" C4 U C 71 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U C 71 " -0.002 2.00e-02 2.50e+03 pdb=" C5 U C 71 " 0.012 2.00e-02 2.50e+03 pdb=" C6 U C 71 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 457 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO B 458 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 458 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 458 " -0.020 5.00e-02 4.00e+02 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 207 2.68 - 3.24: 6870 3.24 - 3.79: 12206 3.79 - 4.35: 15896 4.35 - 4.90: 25105 Nonbonded interactions: 60284 Sorted by model distance: nonbonded pdb=" OG1 THR A 333 " pdb=" OP2 G C 1 " model vdw 2.125 3.040 nonbonded pdb=" OE2 GLU A 352 " pdb=" OG SSA A 601 " model vdw 2.127 3.040 nonbonded pdb=" OE2 GLU B 352 " pdb=" OG SSA B 601 " model vdw 2.144 3.040 nonbonded pdb=" OE2 GLU A 352 " pdb=" N10 SSA A 601 " model vdw 2.243 3.120 nonbonded pdb=" O GLU B 418 " pdb=" NH1 ARG B 459 " model vdw 2.246 3.120 ... (remaining 60279 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: 11.580 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 34.140 Find NCS groups from input model: 0.190 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:3.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 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 : 0.008 0.191 7733 Z= 0.473 Angle : 0.718 20.191 10770 Z= 0.366 Chirality : 0.050 0.549 1235 Planarity : 0.003 0.036 1178 Dihedral : 19.051 162.558 3378 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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 (0.29), residues: 760 helix: 1.87 (0.30), residues: 285 sheet: -1.42 (0.46), residues: 105 loop : -2.11 (0.27), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 409 HIS 0.002 0.000 HIS A 347 PHE 0.007 0.000 PHE A 348 TYR 0.006 0.000 TYR B 230 ARG 0.005 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7346 (mtt180) cc_final: 0.7135 (mtm-85) REVERT: A 218 LYS cc_start: 0.8400 (mtmt) cc_final: 0.7629 (mmmt) REVERT: A 244 ASN cc_start: 0.7760 (m-40) cc_final: 0.7385 (m110) REVERT: A 366 GLN cc_start: 0.7153 (pt0) cc_final: 0.6864 (tm-30) REVERT: A 438 GLN cc_start: 0.8244 (tt0) cc_final: 0.8043 (tt0) REVERT: A 451 ASN cc_start: 0.7540 (p0) cc_final: 0.6953 (p0) REVERT: A 460 LEU cc_start: 0.7512 (mm) cc_final: 0.7277 (mm) REVERT: A 466 GLU cc_start: 0.6244 (mt-10) cc_final: 0.6031 (mt-10) REVERT: B 143 ARG cc_start: 0.6815 (mmm-85) cc_final: 0.5986 (ttm170) REVERT: B 203 ARG cc_start: 0.7968 (mtt90) cc_final: 0.7094 (mtm-85) REVERT: B 313 VAL cc_start: 0.8292 (t) cc_final: 0.8066 (m) REVERT: B 332 GLU cc_start: 0.7442 (tp30) cc_final: 0.7221 (mm-30) REVERT: B 451 ASN cc_start: 0.8027 (p0) cc_final: 0.7425 (p0) REVERT: B 499 GLN cc_start: 0.7939 (tp40) cc_final: 0.7269 (tt0) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3331 time to fit residues: 89.2391 Evaluate side-chains 113 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 217 GLN A 346 HIS A 495 HIS B 448 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.172851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.140189 restraints weight = 8797.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.142982 restraints weight = 4965.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144837 restraints weight = 3426.721| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 7733 Z= 0.414 Angle : 0.705 7.261 10770 Z= 0.353 Chirality : 0.045 0.234 1235 Planarity : 0.005 0.045 1178 Dihedral : 19.109 168.902 1891 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.93 % Allowed : 17.72 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.51 (0.30), residues: 760 helix: 1.60 (0.30), residues: 290 sheet: -0.71 (0.47), residues: 100 loop : -1.91 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 93 HIS 0.006 0.002 HIS A 385 PHE 0.016 0.002 PHE A 245 TYR 0.021 0.002 TYR B 401 ARG 0.007 0.001 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 ASN cc_start: 0.8527 (m-40) cc_final: 0.8119 (m110) REVERT: A 322 MET cc_start: 0.7660 (mpp) cc_final: 0.7385 (mtt) REVERT: B 143 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7060 (ttm170) REVERT: B 309 MET cc_start: 0.8842 (ttt) cc_final: 0.8572 (ttt) REVERT: B 398 LEU cc_start: 0.9105 (mm) cc_final: 0.8840 (mt) outliers start: 32 outliers final: 24 residues processed: 134 average time/residue: 0.2507 time to fit residues: 43.0018 Evaluate side-chains 113 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 51 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.175921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.143748 restraints weight = 8739.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.146609 restraints weight = 4834.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.148458 restraints weight = 3280.648| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7733 Z= 0.162 Angle : 0.508 6.757 10770 Z= 0.255 Chirality : 0.037 0.162 1235 Planarity : 0.004 0.030 1178 Dihedral : 18.923 168.448 1891 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.08 % Allowed : 20.49 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.09 (0.30), residues: 760 helix: 2.12 (0.31), residues: 291 sheet: -0.33 (0.47), residues: 100 loop : -1.61 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 409 HIS 0.005 0.001 HIS A 190 PHE 0.011 0.001 PHE A 371 TYR 0.011 0.001 TYR B 45 ARG 0.013 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 ASN cc_start: 0.8170 (m-40) cc_final: 0.7785 (m110) REVERT: A 307 TYR cc_start: 0.8801 (t80) cc_final: 0.8495 (t80) REVERT: A 322 MET cc_start: 0.7395 (mpp) cc_final: 0.7121 (mtt) REVERT: B 143 ARG cc_start: 0.7952 (mmm-85) cc_final: 0.6982 (ttm170) REVERT: B 498 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8544 (mt) outliers start: 20 outliers final: 12 residues processed: 109 average time/residue: 0.2376 time to fit residues: 33.8512 Evaluate side-chains 100 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 498 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN ** B 375 GLN ** 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 = 0.3969 r_free = 0.3969 target = 0.168279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135755 restraints weight = 8802.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.138329 restraints weight = 5051.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.140025 restraints weight = 3543.486| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7733 Z= 0.336 Angle : 0.621 6.928 10770 Z= 0.312 Chirality : 0.041 0.169 1235 Planarity : 0.005 0.030 1178 Dihedral : 19.037 168.478 1891 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.47 % Allowed : 18.64 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.31 (0.29), residues: 760 helix: 1.57 (0.30), residues: 301 sheet: -0.75 (0.46), residues: 110 loop : -1.68 (0.29), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 409 HIS 0.005 0.001 HIS A 385 PHE 0.020 0.002 PHE A 291 TYR 0.022 0.002 TYR B 45 ARG 0.006 0.001 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 0.805 Fit side-chains REVERT: A 244 ASN cc_start: 0.8267 (m-40) cc_final: 0.7749 (m110) REVERT: A 282 GLN cc_start: 0.7994 (mp10) cc_final: 0.7524 (mt0) REVERT: A 322 MET cc_start: 0.7482 (mpp) cc_final: 0.7261 (mtt) REVERT: B 432 ARG cc_start: 0.7555 (mtt90) cc_final: 0.6947 (mtt180) outliers start: 42 outliers final: 31 residues processed: 120 average time/residue: 0.3181 time to fit residues: 49.2529 Evaluate side-chains 112 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 72 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN ** B 375 GLN ** 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 = 0.4029 r_free = 0.4029 target = 0.173931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142282 restraints weight = 8641.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144932 restraints weight = 4887.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146551 restraints weight = 3370.723| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7733 Z= 0.177 Angle : 0.524 7.069 10770 Z= 0.264 Chirality : 0.037 0.160 1235 Planarity : 0.004 0.032 1178 Dihedral : 18.933 168.110 1891 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.47 % Allowed : 19.88 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.00 (0.30), residues: 760 helix: 1.94 (0.31), residues: 297 sheet: -0.60 (0.46), residues: 110 loop : -1.57 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 409 HIS 0.002 0.001 HIS B 311 PHE 0.014 0.001 PHE A 371 TYR 0.011 0.001 TYR B 230 ARG 0.009 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 1.737 Fit side-chains revert: symmetry clash REVERT: A 244 ASN cc_start: 0.7931 (m-40) cc_final: 0.7415 (m110) REVERT: A 282 GLN cc_start: 0.8008 (mp10) cc_final: 0.7704 (mt0) REVERT: B 64 CYS cc_start: 0.6065 (t) cc_final: 0.5856 (t) REVERT: B 309 MET cc_start: 0.8504 (ttt) cc_final: 0.8191 (ttp) REVERT: B 322 MET cc_start: 0.7498 (mtt) cc_final: 0.7234 (mtt) REVERT: B 432 ARG cc_start: 0.7442 (mtt90) cc_final: 0.7060 (mtt-85) outliers start: 29 outliers final: 20 residues processed: 104 average time/residue: 0.3815 time to fit residues: 55.6689 Evaluate side-chains 97 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.174959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.143185 restraints weight = 8688.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145838 restraints weight = 4921.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147411 restraints weight = 3403.611| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7733 Z= 0.162 Angle : 0.511 7.076 10770 Z= 0.257 Chirality : 0.036 0.159 1235 Planarity : 0.004 0.031 1178 Dihedral : 18.862 167.960 1891 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.31 % Allowed : 19.88 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.26 (0.30), residues: 760 helix: 2.08 (0.31), residues: 297 sheet: -0.27 (0.47), residues: 110 loop : -1.42 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 409 HIS 0.002 0.001 HIS B 240 PHE 0.014 0.001 PHE A 371 TYR 0.010 0.001 TYR B 230 ARG 0.008 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 227 ARG cc_start: 0.7412 (mpp-170) cc_final: 0.7204 (mpp-170) REVERT: A 244 ASN cc_start: 0.7914 (m-40) cc_final: 0.7453 (m110) REVERT: A 282 GLN cc_start: 0.8064 (mp10) cc_final: 0.7761 (mt0) REVERT: A 338 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7726 (pp20) REVERT: B 432 ARG cc_start: 0.7470 (mtt90) cc_final: 0.7047 (mtt-85) REVERT: B 451 ASN cc_start: 0.8303 (p0) cc_final: 0.8052 (p0) outliers start: 28 outliers final: 22 residues processed: 104 average time/residue: 0.2035 time to fit residues: 28.7988 Evaluate side-chains 102 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 16 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.174031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141949 restraints weight = 8649.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144584 restraints weight = 4905.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.146242 restraints weight = 3406.342| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7733 Z= 0.187 Angle : 0.526 7.317 10770 Z= 0.268 Chirality : 0.037 0.159 1235 Planarity : 0.004 0.030 1178 Dihedral : 18.824 167.695 1891 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.31 % Allowed : 20.65 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.37 (0.30), residues: 760 helix: 2.25 (0.31), residues: 291 sheet: -0.14 (0.48), residues: 110 loop : -1.41 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 409 HIS 0.003 0.001 HIS B 240 PHE 0.014 0.001 PHE A 371 TYR 0.012 0.001 TYR B 45 ARG 0.006 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 244 ASN cc_start: 0.7970 (m-40) cc_final: 0.7488 (m110) REVERT: A 282 GLN cc_start: 0.8168 (mp10) cc_final: 0.7856 (mt0) REVERT: A 338 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7986 (pp20) REVERT: B 64 CYS cc_start: 0.6140 (t) cc_final: 0.5898 (t) REVERT: B 432 ARG cc_start: 0.7434 (mtt90) cc_final: 0.7121 (mtt-85) outliers start: 28 outliers final: 22 residues processed: 97 average time/residue: 0.1893 time to fit residues: 25.2040 Evaluate side-chains 98 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 80 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 0.0170 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.170650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138275 restraints weight = 8761.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140959 restraints weight = 4921.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.142694 restraints weight = 3387.367| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7733 Z= 0.220 Angle : 0.545 7.528 10770 Z= 0.276 Chirality : 0.038 0.160 1235 Planarity : 0.004 0.030 1178 Dihedral : 18.828 167.475 1891 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.78 % Allowed : 20.18 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.30 (0.30), residues: 760 helix: 2.19 (0.30), residues: 291 sheet: -0.19 (0.49), residues: 110 loop : -1.44 (0.29), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 409 HIS 0.003 0.001 HIS A 385 PHE 0.015 0.001 PHE A 371 TYR 0.013 0.001 TYR B 45 ARG 0.005 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.692 Fit side-chains REVERT: A 244 ASN cc_start: 0.8049 (m-40) cc_final: 0.7492 (m110) REVERT: A 282 GLN cc_start: 0.7969 (mp10) cc_final: 0.7722 (mt0) REVERT: A 338 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7991 (pp20) REVERT: B 64 CYS cc_start: 0.6102 (t) cc_final: 0.5864 (t) REVERT: B 432 ARG cc_start: 0.7467 (mtt90) cc_final: 0.6893 (mtp85) outliers start: 31 outliers final: 24 residues processed: 101 average time/residue: 0.1879 time to fit residues: 26.0988 Evaluate side-chains 97 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.172420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140489 restraints weight = 8816.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.143125 restraints weight = 5032.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144834 restraints weight = 3493.152| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7733 Z= 0.173 Angle : 0.514 7.614 10770 Z= 0.260 Chirality : 0.037 0.158 1235 Planarity : 0.004 0.030 1178 Dihedral : 18.788 167.314 1891 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.62 % Allowed : 20.49 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: 0.43 (0.30), residues: 760 helix: 2.32 (0.30), residues: 292 sheet: -0.11 (0.48), residues: 110 loop : -1.39 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 409 HIS 0.003 0.001 HIS B 240 PHE 0.012 0.001 PHE A 371 TYR 0.020 0.001 TYR B 153 ARG 0.006 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 244 ASN cc_start: 0.7886 (m-40) cc_final: 0.7464 (m110) REVERT: A 282 GLN cc_start: 0.7957 (mp10) cc_final: 0.7746 (mt0) REVERT: A 338 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7968 (pp20) REVERT: B 64 CYS cc_start: 0.6068 (t) cc_final: 0.5850 (t) REVERT: B 432 ARG cc_start: 0.7376 (mtt90) cc_final: 0.7129 (mtt-85) outliers start: 30 outliers final: 24 residues processed: 99 average time/residue: 0.1951 time to fit residues: 26.2582 Evaluate side-chains 100 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 455 CYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 375 GLN Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 496 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.4617 > 50: distance: 55 - 61: 7.580 distance: 61 - 62: 5.625 distance: 62 - 63: 7.478 distance: 62 - 65: 13.030 distance: 63 - 64: 8.325 distance: 63 - 70: 23.345 distance: 65 - 66: 3.214 distance: 66 - 67: 9.074 distance: 67 - 68: 5.432 distance: 67 - 69: 11.125 distance: 70 - 71: 16.266 distance: 71 - 72: 16.995 distance: 71 - 74: 7.722 distance: 72 - 73: 5.978 distance: 72 - 79: 38.749 distance: 74 - 75: 19.214 distance: 75 - 76: 18.693 distance: 76 - 77: 18.481 distance: 76 - 78: 8.988 distance: 79 - 80: 19.320 distance: 80 - 81: 5.189 distance: 80 - 83: 16.283 distance: 81 - 82: 17.783 distance: 81 - 88: 11.428 distance: 83 - 84: 18.956 distance: 84 - 85: 19.633 distance: 85 - 86: 10.540 distance: 86 - 87: 14.313 distance: 88 - 89: 7.038 distance: 89 - 90: 10.042 distance: 89 - 92: 10.448 distance: 90 - 91: 8.705 distance: 90 - 96: 19.151 distance: 92 - 93: 5.951 distance: 93 - 94: 7.196 distance: 93 - 95: 4.781 distance: 96 - 97: 25.368 distance: 97 - 98: 18.820 distance: 98 - 99: 12.399 distance: 98 - 100: 12.164 distance: 100 - 101: 9.970 distance: 101 - 102: 25.649 distance: 101 - 104: 21.595 distance: 102 - 103: 5.235 distance: 102 - 106: 18.025 distance: 104 - 105: 14.829 distance: 106 - 107: 19.066 distance: 107 - 108: 11.698 distance: 107 - 110: 27.216 distance: 108 - 109: 19.440 distance: 108 - 113: 13.525 distance: 109 - 179: 24.269 distance: 110 - 111: 23.640 distance: 110 - 112: 17.171 distance: 113 - 114: 18.881 distance: 114 - 115: 30.547 distance: 114 - 117: 9.154 distance: 115 - 116: 5.866 distance: 115 - 121: 26.716 distance: 117 - 118: 6.475 distance: 118 - 119: 17.355 distance: 118 - 120: 21.558 distance: 121 - 122: 7.077 distance: 122 - 123: 20.920 distance: 122 - 125: 15.583 distance: 123 - 124: 12.488 distance: 123 - 128: 11.916 distance: 125 - 126: 13.344 distance: 125 - 127: 20.831 distance: 128 - 129: 9.544 distance: 128 - 134: 12.486 distance: 129 - 130: 14.075 distance: 129 - 132: 18.971 distance: 130 - 131: 24.572 distance: 130 - 135: 20.006 distance: 132 - 133: 12.986 distance: 133 - 134: 8.439