Starting phenix.real_space_refine on Tue Feb 3 16:46:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s4j_54566/02_2026/9s4j_54566.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s4j_54566/02_2026/9s4j_54566.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/9s4j_54566/02_2026/9s4j_54566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s4j_54566/02_2026/9s4j_54566.map" model { file = "/net/cci-nas-00/data/ceres_data/9s4j_54566/02_2026/9s4j_54566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s4j_54566/02_2026/9s4j_54566.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 Fe 2 7.16 5 S 10 5.16 5 C 3238 2.51 5 N 829 2.21 5 O 953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1062 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "B" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1116 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 137} Chain: "C" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1521 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 173} Chain: "D" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1247 Classifications: {'peptide': 152} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 143} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.13, per 1000 atoms: 0.22 Number of scatterers: 5032 At special positions: 0 Unit cell: (101.215, 86.3308, 103.2, 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) Fe 2 26.01 S 10 16.00 O 953 8.00 N 829 7.00 C 3238 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 335.6 milliseconds 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1178 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 5 sheets defined 52.0% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 20 through 36 removed outlier: 3.680A pdb=" N PHE A 36 " --> pdb=" O MET A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 43 Processing helix chain 'A' and resid 52 through 72 removed outlier: 3.502A pdb=" N LYS A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 89 removed outlier: 3.949A pdb=" N ASP A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 113 removed outlier: 3.937A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 137 Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.659A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 35 removed outlier: 3.708A pdb=" N TYR B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 42 removed outlier: 3.720A pdb=" N PHE B 41 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 57 through 77 removed outlier: 3.755A pdb=" N HIS B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 85 through 95 removed outlier: 3.693A pdb=" N LYS B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.690A pdb=" N PHE B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 471 through 487 Proline residue: C 483 - end of helix Processing helix chain 'C' and resid 489 through 502 removed outlier: 4.467A pdb=" N GLU C 502 " --> pdb=" O GLU C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 510 removed outlier: 4.182A pdb=" N ALA C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 336 removed outlier: 3.890A pdb=" N LYS D 335 " --> pdb=" O GLN D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.985A pdb=" N ILE D 340 " --> pdb=" O ASN D 336 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 370 Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 471 through 479 Processing sheet with id=AA1, first strand: chain 'C' and resid 349 through 352 Processing sheet with id=AA2, first strand: chain 'C' and resid 349 through 352 removed outlier: 6.813A pdb=" N TYR C 421 " --> pdb=" O TYR C 415 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR C 415 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TYR C 423 " --> pdb=" O VAL C 413 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 354 through 357 removed outlier: 5.018A pdb=" N HIS C 448 " --> pdb=" O TYR C 443 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N TYR C 443 " --> pdb=" O HIS C 448 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASP C 450 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE C 441 " --> pdb=" O ASP C 450 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP C 452 " --> pdb=" O SER C 439 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N SER C 439 " --> pdb=" O ASP C 452 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU C 442 " --> pdb=" O TRP C 396 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TRP C 396 " --> pdb=" O GLU C 442 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 349 through 352 removed outlier: 6.624A pdb=" N GLY D 389 " --> pdb=" O PRO D 374 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR D 380 " --> pdb=" O GLY D 383 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TYR D 421 " --> pdb=" O TYR D 415 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR D 415 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR D 423 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 354 through 357 removed outlier: 4.433A pdb=" N TYR D 453 " --> pdb=" O ILE D 437 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE D 437 " --> pdb=" O TYR D 453 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU D 455 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL D 435 " --> pdb=" O LEU D 455 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 438 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 400 " --> pdb=" O VAL D 438 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLU D 442 " --> pdb=" O TRP D 396 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TRP D 396 " --> pdb=" O GLU D 442 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU D 403 " --> pdb=" O LYS D 406 " (cutoff:3.500A) 263 hydrogen bonds defined for protein. 747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.75 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 2159 1.40 - 1.57: 2988 1.57 - 1.74: 0 1.74 - 1.91: 17 1.91 - 2.08: 8 Bond restraints: 5172 Sorted by residual: bond pdb=" C1D HEM A 201 " pdb=" C2D HEM A 201 " ideal model delta sigma weight residual 1.449 1.356 0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" C3A HEM A 201 " pdb=" C4A HEM A 201 " ideal model delta sigma weight residual 1.449 1.357 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C3C HEM A 201 " pdb=" CAC HEM A 201 " ideal model delta sigma weight residual 1.544 1.453 0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C3B HEM A 201 " pdb=" CAB HEM A 201 " ideal model delta sigma weight residual 1.544 1.457 0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C1A HEM A 201 " pdb=" C2A HEM A 201 " ideal model delta sigma weight residual 1.449 1.365 0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 5167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 6893 1.60 - 3.19: 126 3.19 - 4.79: 27 4.79 - 6.38: 3 6.38 - 7.98: 4 Bond angle restraints: 7053 Sorted by residual: angle pdb=" C3B HEM A 201 " pdb=" CAB HEM A 201 " pdb=" CBB HEM A 201 " ideal model delta sigma weight residual 120.00 127.98 -7.98 3.00e+00 1.11e-01 7.07e+00 angle pdb=" C3C HEM A 201 " pdb=" CAC HEM A 201 " pdb=" CBC HEM A 201 " ideal model delta sigma weight residual 120.00 127.64 -7.64 3.00e+00 1.11e-01 6.49e+00 angle pdb=" C PRO B 36 " pdb=" N TRP B 37 " pdb=" CA TRP B 37 " ideal model delta sigma weight residual 121.54 125.97 -4.43 1.91e+00 2.74e-01 5.37e+00 angle pdb=" CA HIS A 87 " pdb=" C HIS A 87 " pdb=" O HIS A 87 " ideal model delta sigma weight residual 120.42 118.16 2.26 1.06e+00 8.90e-01 4.56e+00 angle pdb=" CA HIS A 72 " pdb=" C HIS A 72 " pdb=" O HIS A 72 " ideal model delta sigma weight residual 121.78 119.45 2.33 1.12e+00 7.97e-01 4.34e+00 ... (remaining 7048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 2853 17.86 - 35.71: 154 35.71 - 53.56: 20 53.56 - 71.42: 7 71.42 - 89.27: 8 Dihedral angle restraints: 3042 sinusoidal: 1216 harmonic: 1826 Sorted by residual: dihedral pdb=" C2C HEM A 201 " pdb=" C3C HEM A 201 " pdb=" CAC HEM A 201 " pdb=" CBC HEM A 201 " ideal model delta sinusoidal sigma weight residual -180.00 -91.11 -88.89 2 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" C2B HEM A 201 " pdb=" C3B HEM A 201 " pdb=" CAB HEM A 201 " pdb=" CBB HEM A 201 " ideal model delta sinusoidal sigma weight residual 0.00 69.38 -69.38 2 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CA GLN D 364 " pdb=" C GLN D 364 " pdb=" N PHE D 365 " pdb=" CA PHE D 365 " ideal model delta harmonic sigma weight residual -180.00 -161.15 -18.85 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 3039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 474 0.030 - 0.059: 202 0.059 - 0.089: 38 0.089 - 0.119: 37 0.119 - 0.148: 7 Chirality restraints: 758 Sorted by residual: chirality pdb=" CA ILE C 441 " pdb=" N ILE C 441 " pdb=" C ILE C 441 " pdb=" CB ILE C 441 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE D 441 " pdb=" N ILE D 441 " pdb=" C ILE D 441 " pdb=" CB ILE D 441 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE C 437 " pdb=" N ILE C 437 " pdb=" C ILE C 437 " pdb=" CB ILE C 437 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 755 not shown) Planarity restraints: 900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 350 " -0.029 5.00e-02 4.00e+02 4.33e-02 2.99e+00 pdb=" N PRO C 351 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 351 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 351 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 118 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO A 119 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 37 " 0.008 2.00e-02 2.50e+03 9.16e-03 2.10e+00 pdb=" CG TRP B 37 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP B 37 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 37 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 37 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 37 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 37 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 37 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 37 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 37 " -0.001 2.00e-02 2.50e+03 ... (remaining 897 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 2631 2.98 - 3.46: 5448 3.46 - 3.94: 7823 3.94 - 4.42: 9275 4.42 - 4.90: 14362 Nonbonded interactions: 39539 Sorted by model distance: nonbonded pdb=" OD1 ASP D 416 " pdb=" OD1 ASP D 418 " model vdw 2.499 3.040 nonbonded pdb=" O LYS C 391 " pdb=" OG1 THR C 392 " model vdw 2.502 3.040 nonbonded pdb=" OD1 ASP B 99 " pdb=" OD1 ASN B 102 " model vdw 2.510 3.040 nonbonded pdb=" OG1 THR D 380 " pdb=" O GLY D 383 " model vdw 2.513 3.040 nonbonded pdb=" O ASN C 465 " pdb=" OD1 ASN C 465 " model vdw 2.517 3.040 ... (remaining 39534 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=0.00 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: 1.190 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.690 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.006 0.128 5174 Z= 0.251 Angle : 0.588 7.976 7053 Z= 0.295 Chirality : 0.040 0.148 758 Planarity : 0.004 0.043 900 Dihedral : 12.138 89.272 1864 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.35), residues: 613 helix: 1.56 (0.32), residues: 270 sheet: 0.26 (0.48), residues: 121 loop : 0.25 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 31 TYR 0.010 0.001 TYR D 469 PHE 0.009 0.001 PHE C 426 TRP 0.025 0.002 TRP B 37 HIS 0.005 0.001 HIS C 448 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 5172) covalent geometry : angle 0.58807 ( 7053) hydrogen bonds : bond 0.13964 ( 255) hydrogen bonds : angle 6.64542 ( 747) Misc. bond : bond 0.11119 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 THR cc_start: 0.8460 (p) cc_final: 0.6822 (p) REVERT: A 137 THR cc_start: 0.9084 (p) cc_final: 0.8848 (p) REVERT: B 4 THR cc_start: 0.9085 (p) cc_final: 0.7528 (p) REVERT: B 45 PHE cc_start: 0.7041 (m-80) cc_final: 0.5943 (m-80) REVERT: B 57 ASN cc_start: 0.8481 (t0) cc_final: 0.8187 (t0) REVERT: B 59 LYS cc_start: 0.9607 (mptt) cc_final: 0.9304 (mppt) REVERT: B 108 ASN cc_start: 0.9290 (m-40) cc_final: 0.8993 (t0) REVERT: C 374 PRO cc_start: 0.7506 (Cg_endo) cc_final: 0.6885 (Cg_exo) REVERT: C 378 ILE cc_start: 0.9003 (pt) cc_final: 0.8707 (tp) REVERT: C 385 ILE cc_start: 0.8941 (mt) cc_final: 0.8681 (mp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1088 time to fit residues: 24.3761 Evaluate side-chains 93 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.2968 r_free = 0.2968 target = 0.039468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.030060 restraints weight = 39706.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.031089 restraints weight = 26600.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.031873 restraints weight = 19899.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.032452 restraints weight = 15888.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.032857 restraints weight = 13404.403| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 5174 Z= 0.202 Angle : 0.656 8.124 7053 Z= 0.338 Chirality : 0.044 0.170 758 Planarity : 0.005 0.058 900 Dihedral : 9.192 88.139 681 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.35), residues: 613 helix: 1.28 (0.31), residues: 280 sheet: 0.10 (0.48), residues: 121 loop : 0.60 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 425 TYR 0.025 0.002 TYR A 24 PHE 0.028 0.003 PHE D 458 TRP 0.015 0.002 TRP A 14 HIS 0.005 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00508 ( 5172) covalent geometry : angle 0.65648 ( 7053) hydrogen bonds : bond 0.03618 ( 255) hydrogen bonds : angle 5.07845 ( 747) Misc. bond : bond 0.06027 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8781 (m-80) cc_final: 0.8146 (m-80) REVERT: A 29 LEU cc_start: 0.9849 (mt) cc_final: 0.9563 (mt) REVERT: A 32 MET cc_start: 0.9224 (tpt) cc_final: 0.8853 (tpt) REVERT: A 42 TYR cc_start: 0.9437 (m-10) cc_final: 0.9236 (m-10) REVERT: A 72 HIS cc_start: 0.9298 (m90) cc_final: 0.8973 (m90) REVERT: A 75 ASP cc_start: 0.9557 (t0) cc_final: 0.9189 (t0) REVERT: A 104 CYS cc_start: 0.9220 (m) cc_final: 0.8786 (m) REVERT: A 116 GLU cc_start: 0.9322 (mp0) cc_final: 0.9089 (mp0) REVERT: B 7 GLU cc_start: 0.9467 (mt-10) cc_final: 0.9242 (mt-10) REVERT: B 45 PHE cc_start: 0.8654 (m-80) cc_final: 0.7810 (m-80) REVERT: B 57 ASN cc_start: 0.9106 (t0) cc_final: 0.8452 (t0) REVERT: B 59 LYS cc_start: 0.9791 (mptt) cc_final: 0.9554 (mppt) REVERT: B 73 ASP cc_start: 0.9458 (t0) cc_final: 0.9197 (t0) REVERT: B 85 PHE cc_start: 0.9236 (m-10) cc_final: 0.9014 (m-80) REVERT: B 108 ASN cc_start: 0.9477 (m-40) cc_final: 0.9044 (t0) REVERT: B 131 GLN cc_start: 0.9668 (mm-40) cc_final: 0.9239 (mm-40) REVERT: C 355 GLN cc_start: 0.9289 (mp10) cc_final: 0.9016 (mp10) REVERT: C 356 MET cc_start: 0.9261 (mmp) cc_final: 0.8917 (mmm) REVERT: C 365 PHE cc_start: 0.8977 (t80) cc_final: 0.8748 (t80) REVERT: C 425 ARG cc_start: 0.8204 (mtp-110) cc_final: 0.7773 (mtp-110) REVERT: C 476 ASN cc_start: 0.9454 (m110) cc_final: 0.9220 (m110) REVERT: D 356 MET cc_start: 0.9478 (mmm) cc_final: 0.8954 (mmm) REVERT: D 458 PHE cc_start: 0.8607 (m-10) cc_final: 0.7873 (m-80) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0989 time to fit residues: 12.6197 Evaluate side-chains 74 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 58 optimal weight: 0.4980 chunk 54 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 367 HIS ** 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 = 0.2922 r_free = 0.2922 target = 0.037853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.028561 restraints weight = 39176.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.029589 restraints weight = 26405.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.030312 restraints weight = 19825.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.030892 restraints weight = 16013.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.031325 restraints weight = 13482.535| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 5174 Z= 0.202 Angle : 0.638 8.438 7053 Z= 0.319 Chirality : 0.042 0.147 758 Planarity : 0.005 0.050 900 Dihedral : 9.219 88.303 681 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.35), residues: 613 helix: 1.02 (0.31), residues: 288 sheet: -0.17 (0.47), residues: 134 loop : 0.86 (0.50), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 31 TYR 0.022 0.002 TYR A 24 PHE 0.019 0.002 PHE C 426 TRP 0.009 0.001 TRP D 349 HIS 0.007 0.001 HIS D 448 Details of bonding type rmsd covalent geometry : bond 0.00505 ( 5172) covalent geometry : angle 0.63811 ( 7053) hydrogen bonds : bond 0.03484 ( 255) hydrogen bonds : angle 5.03025 ( 747) Misc. bond : bond 0.10795 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.9883 (mt) cc_final: 0.9602 (mt) REVERT: A 75 ASP cc_start: 0.9567 (t0) cc_final: 0.9186 (t0) REVERT: A 116 GLU cc_start: 0.9396 (mp0) cc_final: 0.8995 (mp0) REVERT: B 45 PHE cc_start: 0.8741 (m-80) cc_final: 0.7547 (m-80) REVERT: B 57 ASN cc_start: 0.9047 (t0) cc_final: 0.8135 (t0) REVERT: B 59 LYS cc_start: 0.9795 (mptt) cc_final: 0.9322 (mppt) REVERT: B 73 ASP cc_start: 0.9471 (t0) cc_final: 0.9205 (t0) REVERT: B 85 PHE cc_start: 0.9443 (m-10) cc_final: 0.9017 (m-80) REVERT: B 104 ARG cc_start: 0.9144 (mtm-85) cc_final: 0.8916 (mtt-85) REVERT: B 108 ASN cc_start: 0.9500 (m-40) cc_final: 0.9110 (t0) REVERT: B 131 GLN cc_start: 0.9686 (mm-40) cc_final: 0.9442 (mm-40) REVERT: B 139 ASN cc_start: 0.9699 (m110) cc_final: 0.9435 (t0) REVERT: C 355 GLN cc_start: 0.9309 (mp10) cc_final: 0.9076 (mp10) REVERT: C 364 GLN cc_start: 0.9209 (tm-30) cc_final: 0.8769 (tm-30) REVERT: C 365 PHE cc_start: 0.9045 (t80) cc_final: 0.8698 (t80) REVERT: C 426 PHE cc_start: 0.9682 (p90) cc_final: 0.9405 (p90) REVERT: C 476 ASN cc_start: 0.9473 (m110) cc_final: 0.9259 (m110) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0915 time to fit residues: 10.6595 Evaluate side-chains 74 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 56 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 358 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.038538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.029227 restraints weight = 39009.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.030238 restraints weight = 26498.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.030982 restraints weight = 19917.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.031541 restraints weight = 16089.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.031998 restraints weight = 13603.006| |-----------------------------------------------------------------------------| r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 5174 Z= 0.154 Angle : 0.596 6.600 7053 Z= 0.301 Chirality : 0.042 0.162 758 Planarity : 0.005 0.059 900 Dihedral : 9.194 89.824 681 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.35), residues: 613 helix: 1.06 (0.31), residues: 286 sheet: -0.20 (0.47), residues: 133 loop : 0.66 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 31 TYR 0.014 0.001 TYR A 24 PHE 0.022 0.002 PHE C 426 TRP 0.007 0.001 TRP B 37 HIS 0.005 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 5172) covalent geometry : angle 0.59619 ( 7053) hydrogen bonds : bond 0.03221 ( 255) hydrogen bonds : angle 4.89281 ( 747) Misc. bond : bond 0.11185 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.9585 (t0) cc_final: 0.9151 (t0) REVERT: A 116 GLU cc_start: 0.9366 (mp0) cc_final: 0.8997 (mp0) REVERT: B 7 GLU cc_start: 0.9416 (pt0) cc_final: 0.9127 (pp20) REVERT: B 57 ASN cc_start: 0.9124 (t0) cc_final: 0.8476 (t0) REVERT: B 59 LYS cc_start: 0.9803 (mptt) cc_final: 0.9541 (mppt) REVERT: B 73 ASP cc_start: 0.9448 (t0) cc_final: 0.9161 (t0) REVERT: B 85 PHE cc_start: 0.9484 (m-10) cc_final: 0.9104 (m-80) REVERT: B 104 ARG cc_start: 0.9147 (mtm-85) cc_final: 0.8905 (mtt-85) REVERT: B 108 ASN cc_start: 0.9502 (m-40) cc_final: 0.9095 (t0) REVERT: B 131 GLN cc_start: 0.9714 (mm-40) cc_final: 0.9450 (mm-40) REVERT: C 364 GLN cc_start: 0.9193 (tm-30) cc_final: 0.8770 (tm-30) REVERT: C 365 PHE cc_start: 0.9015 (t80) cc_final: 0.8771 (t80) REVERT: C 388 LEU cc_start: 0.9478 (tp) cc_final: 0.9274 (tp) REVERT: C 426 PHE cc_start: 0.9614 (p90) cc_final: 0.9190 (p90) REVERT: C 456 MET cc_start: 0.9480 (tpt) cc_final: 0.9182 (tpp) REVERT: C 476 ASN cc_start: 0.9467 (m110) cc_final: 0.9249 (m110) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0946 time to fit residues: 10.6221 Evaluate side-chains 67 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.036666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.027705 restraints weight = 41120.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.028726 restraints weight = 26992.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.029487 restraints weight = 19948.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.030034 restraints weight = 15876.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.030485 restraints weight = 13323.227| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.203 5174 Z= 0.233 Angle : 0.659 8.614 7053 Z= 0.328 Chirality : 0.042 0.132 758 Planarity : 0.005 0.065 900 Dihedral : 9.044 88.652 681 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.19 % Allowed : 1.87 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.35), residues: 613 helix: 1.03 (0.31), residues: 287 sheet: -0.25 (0.49), residues: 124 loop : 0.30 (0.47), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 31 TYR 0.018 0.002 TYR D 451 PHE 0.023 0.003 PHE D 458 TRP 0.011 0.002 TRP A 14 HIS 0.006 0.002 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 5172) covalent geometry : angle 0.65884 ( 7053) hydrogen bonds : bond 0.03399 ( 255) hydrogen bonds : angle 4.98838 ( 747) Misc. bond : bond 0.19031 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.9465 (m-10) cc_final: 0.9260 (m-10) REVERT: A 116 GLU cc_start: 0.9359 (mp0) cc_final: 0.8954 (mp0) REVERT: B 57 ASN cc_start: 0.9132 (t0) cc_final: 0.8479 (t0) REVERT: B 59 LYS cc_start: 0.9807 (mptt) cc_final: 0.9550 (mppt) REVERT: B 73 ASP cc_start: 0.9470 (t0) cc_final: 0.9182 (t0) REVERT: B 104 ARG cc_start: 0.9136 (mtm-85) cc_final: 0.8906 (mtt-85) REVERT: B 108 ASN cc_start: 0.9529 (m-40) cc_final: 0.9098 (t0) REVERT: B 131 GLN cc_start: 0.9712 (mm-40) cc_final: 0.9427 (mm-40) REVERT: C 355 GLN cc_start: 0.9267 (mp10) cc_final: 0.9044 (mp10) REVERT: C 356 MET cc_start: 0.9322 (mmp) cc_final: 0.9112 (mmm) REVERT: C 364 GLN cc_start: 0.9260 (tm-30) cc_final: 0.8843 (tm-30) REVERT: C 365 PHE cc_start: 0.9153 (t80) cc_final: 0.8879 (t80) REVERT: C 388 LEU cc_start: 0.9486 (tp) cc_final: 0.9203 (tp) REVERT: C 456 MET cc_start: 0.9601 (tpt) cc_final: 0.9224 (tpp) REVERT: C 458 PHE cc_start: 0.9609 (m-80) cc_final: 0.9261 (m-80) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.0883 time to fit residues: 9.0505 Evaluate side-chains 58 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN D 348 ASN ** D 367 HIS ** 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 = 0.2935 r_free = 0.2935 target = 0.038091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.028923 restraints weight = 39586.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.029979 restraints weight = 25992.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.030788 restraints weight = 19187.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.031380 restraints weight = 15211.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.031796 restraints weight = 12687.066| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 5174 Z= 0.114 Angle : 0.563 5.844 7053 Z= 0.282 Chirality : 0.041 0.133 758 Planarity : 0.005 0.067 900 Dihedral : 8.862 84.485 681 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.35), residues: 613 helix: 1.14 (0.31), residues: 282 sheet: -0.43 (0.47), residues: 134 loop : 0.65 (0.46), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 31 TYR 0.011 0.001 TYR A 140 PHE 0.019 0.002 PHE D 458 TRP 0.007 0.001 TRP B 37 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 5172) covalent geometry : angle 0.56312 ( 7053) hydrogen bonds : bond 0.03012 ( 255) hydrogen bonds : angle 4.60421 ( 747) Misc. bond : bond 0.09038 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 PHE cc_start: 0.9282 (m-80) cc_final: 0.8996 (m-80) REVERT: A 116 GLU cc_start: 0.9307 (mp0) cc_final: 0.9012 (mp0) REVERT: B 57 ASN cc_start: 0.9127 (t0) cc_final: 0.8539 (t0) REVERT: B 59 LYS cc_start: 0.9802 (mptt) cc_final: 0.9542 (mppt) REVERT: B 73 ASP cc_start: 0.9427 (t0) cc_final: 0.9126 (t0) REVERT: B 85 PHE cc_start: 0.9536 (m-10) cc_final: 0.9049 (m-80) REVERT: B 108 ASN cc_start: 0.9499 (m-40) cc_final: 0.9106 (t0) REVERT: B 131 GLN cc_start: 0.9743 (mm-40) cc_final: 0.9440 (mm-40) REVERT: C 355 GLN cc_start: 0.9286 (mp10) cc_final: 0.9060 (mp10) REVERT: C 364 GLN cc_start: 0.9248 (tm-30) cc_final: 0.8789 (tm-30) REVERT: C 365 PHE cc_start: 0.9086 (t80) cc_final: 0.8779 (t80) REVERT: C 388 LEU cc_start: 0.9440 (tp) cc_final: 0.9165 (tp) REVERT: C 426 PHE cc_start: 0.9540 (p90) cc_final: 0.8971 (p90) REVERT: C 456 MET cc_start: 0.9531 (tpt) cc_final: 0.9234 (tpp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0998 time to fit residues: 10.9232 Evaluate side-chains 62 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 11 optimal weight: 0.0980 chunk 23 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.038165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.029103 restraints weight = 38716.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.030141 restraints weight = 25535.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.030918 restraints weight = 18971.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.031490 restraints weight = 15143.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.031846 restraints weight = 12702.949| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 5174 Z= 0.116 Angle : 0.604 8.782 7053 Z= 0.299 Chirality : 0.042 0.175 758 Planarity : 0.005 0.068 900 Dihedral : 8.727 83.452 681 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.35), residues: 613 helix: 1.23 (0.31), residues: 282 sheet: -0.53 (0.46), residues: 133 loop : 0.61 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 31 TYR 0.008 0.001 TYR A 24 PHE 0.019 0.002 PHE D 458 TRP 0.015 0.001 TRP A 14 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5172) covalent geometry : angle 0.60381 ( 7053) hydrogen bonds : bond 0.03095 ( 255) hydrogen bonds : angle 4.65759 ( 747) Misc. bond : bond 0.08881 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 PHE cc_start: 0.9329 (m-80) cc_final: 0.9089 (m-80) REVERT: A 42 TYR cc_start: 0.9388 (m-10) cc_final: 0.9159 (m-10) REVERT: A 116 GLU cc_start: 0.9267 (mp0) cc_final: 0.8979 (mp0) REVERT: B 57 ASN cc_start: 0.9059 (t0) cc_final: 0.8529 (t0) REVERT: B 59 LYS cc_start: 0.9805 (mptt) cc_final: 0.9545 (mppt) REVERT: B 73 ASP cc_start: 0.9420 (t0) cc_final: 0.9139 (t0) REVERT: B 108 ASN cc_start: 0.9501 (m-40) cc_final: 0.9088 (t0) REVERT: B 131 GLN cc_start: 0.9752 (mm-40) cc_final: 0.9457 (mm-40) REVERT: C 364 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8759 (tm-30) REVERT: C 365 PHE cc_start: 0.9081 (t80) cc_final: 0.8821 (t80) REVERT: C 387 GLU cc_start: 0.8692 (tt0) cc_final: 0.7213 (tp30) REVERT: C 424 ILE cc_start: 0.9701 (pt) cc_final: 0.8844 (tp) REVERT: C 456 MET cc_start: 0.9502 (tpt) cc_final: 0.9241 (tpp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0917 time to fit residues: 10.1311 Evaluate side-chains 66 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.037987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.028979 restraints weight = 39461.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.030007 restraints weight = 25767.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.030792 restraints weight = 19083.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.031387 restraints weight = 15166.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.031846 restraints weight = 12648.515| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 5174 Z= 0.123 Angle : 0.607 7.316 7053 Z= 0.303 Chirality : 0.042 0.149 758 Planarity : 0.005 0.068 900 Dihedral : 8.617 83.112 681 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.35), residues: 613 helix: 1.31 (0.32), residues: 282 sheet: -0.45 (0.46), residues: 133 loop : 0.49 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 425 TYR 0.014 0.001 TYR C 423 PHE 0.031 0.002 PHE C 426 TRP 0.008 0.001 TRP B 37 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 5172) covalent geometry : angle 0.60677 ( 7053) hydrogen bonds : bond 0.03197 ( 255) hydrogen bonds : angle 4.53876 ( 747) Misc. bond : bond 0.09339 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 PHE cc_start: 0.9346 (m-80) cc_final: 0.9115 (m-80) REVERT: A 116 GLU cc_start: 0.9254 (mp0) cc_final: 0.8933 (mp0) REVERT: B 57 ASN cc_start: 0.9069 (t0) cc_final: 0.8558 (t0) REVERT: B 59 LYS cc_start: 0.9806 (mptt) cc_final: 0.9548 (mppt) REVERT: B 73 ASP cc_start: 0.9420 (t0) cc_final: 0.9140 (t0) REVERT: B 104 ARG cc_start: 0.9180 (mtm-85) cc_final: 0.8874 (mtt-85) REVERT: B 108 ASN cc_start: 0.9505 (m-40) cc_final: 0.9091 (t0) REVERT: B 131 GLN cc_start: 0.9756 (mm-40) cc_final: 0.9480 (mm-40) REVERT: C 364 GLN cc_start: 0.9164 (tm-30) cc_final: 0.8719 (tm-30) REVERT: C 365 PHE cc_start: 0.9074 (t80) cc_final: 0.8825 (t80) REVERT: C 388 LEU cc_start: 0.9454 (tp) cc_final: 0.9241 (tp) REVERT: C 456 MET cc_start: 0.9514 (tpt) cc_final: 0.9243 (tpp) REVERT: D 458 PHE cc_start: 0.9013 (m-80) cc_final: 0.8669 (m-80) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0971 time to fit residues: 9.8226 Evaluate side-chains 63 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.037280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.028267 restraints weight = 39826.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.029281 restraints weight = 26305.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.030052 restraints weight = 19538.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.030615 restraints weight = 15605.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.030952 restraints weight = 13099.228| |-----------------------------------------------------------------------------| r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 5174 Z= 0.134 Angle : 0.596 6.573 7053 Z= 0.296 Chirality : 0.042 0.230 758 Planarity : 0.005 0.067 900 Dihedral : 8.511 82.902 681 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.35), residues: 613 helix: 1.37 (0.31), residues: 282 sheet: -0.54 (0.46), residues: 133 loop : 0.50 (0.46), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 31 TYR 0.010 0.001 TYR C 475 PHE 0.032 0.002 PHE C 426 TRP 0.014 0.001 TRP A 14 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 5172) covalent geometry : angle 0.59565 ( 7053) hydrogen bonds : bond 0.02943 ( 255) hydrogen bonds : angle 4.53862 ( 747) Misc. bond : bond 0.11474 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 PHE cc_start: 0.9398 (m-80) cc_final: 0.9178 (m-80) REVERT: A 116 GLU cc_start: 0.9260 (mp0) cc_final: 0.8919 (mp0) REVERT: B 57 ASN cc_start: 0.9078 (t0) cc_final: 0.8596 (t0) REVERT: B 59 LYS cc_start: 0.9804 (mptt) cc_final: 0.9545 (mppt) REVERT: B 73 ASP cc_start: 0.9432 (t0) cc_final: 0.9149 (t0) REVERT: B 104 ARG cc_start: 0.9189 (mtm-85) cc_final: 0.8876 (mtt-85) REVERT: B 108 ASN cc_start: 0.9509 (m-40) cc_final: 0.9075 (t0) REVERT: B 131 GLN cc_start: 0.9757 (mm-40) cc_final: 0.9466 (mm-40) REVERT: C 364 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8718 (tm-30) REVERT: C 365 PHE cc_start: 0.9134 (t80) cc_final: 0.8931 (t80) REVERT: C 388 LEU cc_start: 0.9467 (tp) cc_final: 0.9205 (tp) REVERT: C 456 MET cc_start: 0.9516 (tpt) cc_final: 0.9225 (tpp) REVERT: D 456 MET cc_start: 0.9156 (tmm) cc_final: 0.8737 (tmm) REVERT: D 458 PHE cc_start: 0.9025 (m-80) cc_final: 0.8353 (m-80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0971 time to fit residues: 10.0687 Evaluate side-chains 63 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN ** D 367 HIS ** 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 = 0.2936 r_free = 0.2936 target = 0.037744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.028655 restraints weight = 40121.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.029680 restraints weight = 26445.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.030458 restraints weight = 19673.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.031025 restraints weight = 15679.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.031443 restraints weight = 13187.029| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 5174 Z= 0.116 Angle : 0.586 7.201 7053 Z= 0.291 Chirality : 0.042 0.186 758 Planarity : 0.005 0.067 900 Dihedral : 8.434 83.138 681 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.35), residues: 613 helix: 1.38 (0.32), residues: 283 sheet: -0.53 (0.47), residues: 128 loop : 0.37 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 425 TYR 0.010 0.001 TYR C 475 PHE 0.010 0.002 PHE C 365 TRP 0.008 0.001 TRP B 37 HIS 0.003 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5172) covalent geometry : angle 0.58598 ( 7053) hydrogen bonds : bond 0.02872 ( 255) hydrogen bonds : angle 4.45932 ( 747) Misc. bond : bond 0.09040 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9628 (ptpt) cc_final: 0.9173 (pttm) REVERT: A 116 GLU cc_start: 0.9224 (mp0) cc_final: 0.8933 (mp0) REVERT: B 57 ASN cc_start: 0.9058 (t0) cc_final: 0.8554 (t0) REVERT: B 59 LYS cc_start: 0.9803 (mptt) cc_final: 0.9547 (mppt) REVERT: B 73 ASP cc_start: 0.9441 (t0) cc_final: 0.9164 (t0) REVERT: B 104 ARG cc_start: 0.9188 (mtm-85) cc_final: 0.8876 (mtt-85) REVERT: B 108 ASN cc_start: 0.9505 (m-40) cc_final: 0.9065 (t0) REVERT: B 131 GLN cc_start: 0.9765 (mm-40) cc_final: 0.9490 (mm-40) REVERT: C 364 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8627 (tm-30) REVERT: C 365 PHE cc_start: 0.9063 (t80) cc_final: 0.8845 (t80) REVERT: C 456 MET cc_start: 0.9497 (tpt) cc_final: 0.9186 (tpp) REVERT: D 456 MET cc_start: 0.9161 (tmm) cc_final: 0.8820 (tmm) REVERT: D 458 PHE cc_start: 0.9020 (m-80) cc_final: 0.8369 (m-80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0699 time to fit residues: 7.2397 Evaluate side-chains 63 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 34 optimal weight: 0.0670 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 56 optimal weight: 0.0470 chunk 28 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 ASN ** D 367 HIS ** 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 = 0.2951 r_free = 0.2951 target = 0.038493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.029348 restraints weight = 39610.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.030407 restraints weight = 26073.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.031210 restraints weight = 19356.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.031789 restraints weight = 15397.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.032228 restraints weight = 12903.460| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 5174 Z= 0.108 Angle : 0.599 7.379 7053 Z= 0.295 Chirality : 0.043 0.207 758 Planarity : 0.005 0.067 900 Dihedral : 8.404 84.314 681 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.35), residues: 613 helix: 1.40 (0.32), residues: 277 sheet: -0.45 (0.48), residues: 128 loop : 0.47 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 31 TYR 0.009 0.001 TYR C 475 PHE 0.029 0.002 PHE C 426 TRP 0.032 0.002 TRP A 14 HIS 0.003 0.000 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 5172) covalent geometry : angle 0.59946 ( 7053) hydrogen bonds : bond 0.02915 ( 255) hydrogen bonds : angle 4.40550 ( 747) Misc. bond : bond 0.05276 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1064.97 seconds wall clock time: 19 minutes 5.96 seconds (1145.96 seconds total)