Starting phenix.real_space_refine on Wed Jun 3 13:45:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wmd_66087/06_2026/9wmd_66087.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wmd_66087/06_2026/9wmd_66087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wmd_66087/06_2026/9wmd_66087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wmd_66087/06_2026/9wmd_66087.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wmd_66087/06_2026/9wmd_66087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wmd_66087/06_2026/9wmd_66087.map" } resolution = 3.59 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= 0.009 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 3919 2.51 5 N 1018 2.21 5 O 1083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6036 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6036 Classifications: {'peptide': 741} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 707} Chain breaks: 1 Time building chain proxies: 1.54, per 1000 atoms: 0.26 Number of scatterers: 6036 At special positions: 0 Unit cell: (82, 86.1, 104.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 1083 8.00 N 1018 7.00 C 3919 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: 0.47 Conformation dependent library (CDL) restraints added in 461.3 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 8 sheets defined 33.2% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 37 through 48 removed outlier: 3.775A pdb=" N GLN A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 105 through 126 removed outlier: 3.733A pdb=" N ASP A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL A 111 " --> pdb=" O HIS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.633A pdb=" N TYR A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.548A pdb=" N LYS A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 366 through 369 Processing helix chain 'A' and resid 370 through 383 Processing helix chain 'A' and resid 404 through 423 Processing helix chain 'A' and resid 441 through 457 Processing helix chain 'A' and resid 474 through 489 removed outlier: 3.513A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 524 through 546 removed outlier: 4.320A pdb=" N GLY A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ARG A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 541 " --> pdb=" O TYR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 624 removed outlier: 3.559A pdb=" N LEU A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 640 through 656 removed outlier: 3.748A pdb=" N GLU A 656 " --> pdb=" O THR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 748 Processing helix chain 'A' and resid 761 through 772 Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 132 removed outlier: 5.626A pdb=" N GLU A 155 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE A 169 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASN A 7 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 12.881A pdb=" N LEU A 175 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 17.428A pdb=" N ILE A 5 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 25.640A pdb=" N THR A 177 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 30.654A pdb=" N ASP A 3 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 339 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 8 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU A 337 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG A 10 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 281 removed outlier: 4.485A pdb=" N SER A 265 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY A 221 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR A 269 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU A 219 " --> pdb=" O THR A 269 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG A 205 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET A 287 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 181 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR A 179 " --> pdb=" O TYR A 289 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE A 169 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASN A 7 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 12.881A pdb=" N LEU A 175 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 17.428A pdb=" N ILE A 5 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 25.640A pdb=" N THR A 177 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 30.654A pdb=" N ASP A 3 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 62 removed outlier: 7.206A pdb=" N PHE A 66 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N PHE A 26 " --> pdb=" O PHE A 66 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 68 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU A 23 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU A 95 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASP A 25 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 93 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 327 Processing sheet with id=AA5, first strand: chain 'A' and resid 358 through 359 Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 6.688A pdb=" N TYR A 394 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL A 466 " --> pdb=" O TYR A 394 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU A 396 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 507 through 511 Processing sheet with id=AA8, first strand: chain 'A' and resid 583 through 590 removed outlier: 4.191A pdb=" N GLN A 583 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N VAL A 567 " --> pdb=" O ASP A 635 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 630 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL A 669 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 632 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 671 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG A 634 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR A 666 " --> pdb=" O GLY A 732 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY A 732 " --> pdb=" O TYR A 666 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 668 " --> pdb=" O LYS A 730 " (cutoff:3.500A) 270 hydrogen bonds defined for protein. 756 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: 1.14 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: 1.22 - 1.34: 1917 1.34 - 1.46: 1250 1.46 - 1.58: 2986 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 6181 Sorted by residual: bond pdb=" CG PRO A 491 " pdb=" CD PRO A 491 " ideal model delta sigma weight residual 1.512 1.481 0.031 2.70e-02 1.37e+03 1.35e+00 bond pdb=" CB PRO A 491 " pdb=" CG PRO A 491 " ideal model delta sigma weight residual 1.506 1.471 0.035 3.90e-02 6.57e+02 8.13e-01 bond pdb=" N ALA A 753 " pdb=" CA ALA A 753 " ideal model delta sigma weight residual 1.463 1.455 0.007 8.80e-03 1.29e+04 7.18e-01 bond pdb=" C HIS A 587 " pdb=" O HIS A 587 " ideal model delta sigma weight residual 1.248 1.238 0.011 1.26e-02 6.30e+03 7.09e-01 bond pdb=" CA MET A 266 " pdb=" CB MET A 266 " ideal model delta sigma weight residual 1.533 1.549 -0.016 1.90e-02 2.77e+03 6.96e-01 ... (remaining 6176 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 8078 1.73 - 3.46: 229 3.46 - 5.19: 30 5.19 - 6.91: 8 6.91 - 8.64: 2 Bond angle restraints: 8347 Sorted by residual: angle pdb=" C ASN A 328 " pdb=" CA ASN A 328 " pdb=" CB ASN A 328 " ideal model delta sigma weight residual 116.54 110.63 5.91 1.15e+00 7.56e-01 2.64e+01 angle pdb=" C TYR A 490 " pdb=" N PRO A 491 " pdb=" CD PRO A 491 " ideal model delta sigma weight residual 120.60 111.96 8.64 2.20e+00 2.07e-01 1.54e+01 angle pdb=" CA ASN A 328 " pdb=" C ASN A 328 " pdb=" N ALA A 329 " ideal model delta sigma weight residual 119.52 116.94 2.58 7.90e-01 1.60e+00 1.07e+01 angle pdb=" N GLU A 448 " pdb=" CA GLU A 448 " pdb=" CB GLU A 448 " ideal model delta sigma weight residual 110.12 114.37 -4.25 1.47e+00 4.63e-01 8.34e+00 angle pdb=" CA GLN A 690 " pdb=" CB GLN A 690 " pdb=" CG GLN A 690 " ideal model delta sigma weight residual 114.10 119.77 -5.67 2.00e+00 2.50e-01 8.05e+00 ... (remaining 8342 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3394 17.69 - 35.38: 253 35.38 - 53.06: 51 53.06 - 70.75: 12 70.75 - 88.44: 8 Dihedral angle restraints: 3718 sinusoidal: 1538 harmonic: 2180 Sorted by residual: dihedral pdb=" CB GLU A 525 " pdb=" CG GLU A 525 " pdb=" CD GLU A 525 " pdb=" OE1 GLU A 525 " ideal model delta sinusoidal sigma weight residual 0.00 88.44 -88.44 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU A 16 " pdb=" CG GLU A 16 " pdb=" CD GLU A 16 " pdb=" OE1 GLU A 16 " ideal model delta sinusoidal sigma weight residual 0.00 -87.49 87.49 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA LEU A 8 " pdb=" C LEU A 8 " pdb=" N TYR A 9 " pdb=" CA TYR A 9 " ideal model delta harmonic sigma weight residual -180.00 -165.02 -14.98 0 5.00e+00 4.00e-02 8.98e+00 ... (remaining 3715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 517 0.030 - 0.059: 258 0.059 - 0.089: 69 0.089 - 0.118: 52 0.118 - 0.148: 13 Chirality restraints: 909 Sorted by residual: chirality pdb=" CA GLN A 690 " pdb=" N GLN A 690 " pdb=" C GLN A 690 " pdb=" CB GLN A 690 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA ILE A 151 " pdb=" N ILE A 151 " pdb=" C ILE A 151 " pdb=" CB ILE A 151 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA VAL A 70 " pdb=" N VAL A 70 " pdb=" C VAL A 70 " pdb=" CB VAL A 70 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 906 not shown) Planarity restraints: 1067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 490 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.54e+00 pdb=" N PRO A 491 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 772 " -0.041 5.00e-02 4.00e+02 6.28e-02 6.30e+00 pdb=" N PRO A 773 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 773 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 773 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 84 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO A 85 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.020 5.00e-02 4.00e+02 ... (remaining 1064 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 334 2.73 - 3.27: 6176 3.27 - 3.82: 9977 3.82 - 4.36: 12046 4.36 - 4.90: 20754 Nonbonded interactions: 49287 Sorted by model distance: nonbonded pdb=" O ILE A 45 " pdb=" OG SER A 50 " model vdw 2.190 3.040 nonbonded pdb=" NH1 ARG A 375 " pdb=" O MET A 748 " model vdw 2.211 3.120 nonbonded pdb=" OG1 THR A 274 " pdb=" OE1 GLN A 598 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR A 512 " pdb=" OE2 GLU A 520 " model vdw 2.262 3.040 nonbonded pdb=" O SER A 443 " pdb=" NE2 GLN A 447 " model vdw 2.270 3.120 ... (remaining 49282 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.680 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.960 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 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 : 0.003 0.035 6181 Z= 0.159 Angle : 0.695 8.643 8347 Z= 0.389 Chirality : 0.043 0.148 909 Planarity : 0.005 0.073 1067 Dihedral : 14.035 88.441 2314 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.53 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.29 (0.31), residues: 737 helix: 0.50 (0.37), residues: 205 sheet: -0.01 (0.42), residues: 149 loop : -0.57 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.022 0.001 TYR A 490 PHE 0.021 0.002 PHE A 481 TRP 0.016 0.002 TRP A 131 HIS 0.006 0.001 HIS A 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 ( 6181) covalent geometry : angle 0.69511 / 0.39 ( 8347) hydrogen bonds : bond 0.15956 / 10.54 ( 266) hydrogen bonds : angle 7.54620 / 5.41 ( 756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ILE cc_start: 0.8042 (mm) cc_final: 0.7744 (mm) REVERT: A 113 TYR cc_start: 0.7824 (t80) cc_final: 0.7112 (t80) REVERT: A 429 PHE cc_start: 0.6580 (m-80) cc_final: 0.6171 (m-80) REVERT: A 467 LEU cc_start: 0.8524 (mp) cc_final: 0.8037 (mt) REVERT: A 481 PHE cc_start: 0.7831 (t80) cc_final: 0.7622 (t80) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1015 time to fit residues: 27.9891 Evaluate side-chains 145 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 213 ASN A 315 ASN ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.073642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.053097 restraints weight = 24266.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.054981 restraints weight = 15540.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.056342 restraints weight = 11386.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.057325 restraints weight = 9089.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.058048 restraints weight = 7686.599| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6181 Z= 0.151 Angle : 0.751 9.817 8347 Z= 0.379 Chirality : 0.047 0.185 909 Planarity : 0.005 0.059 1067 Dihedral : 4.671 20.022 811 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.85 % Favored : 96.88 % Rotamer: Outliers : 2.11 % Allowed : 12.39 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.39 (0.30), residues: 737 helix: 0.46 (0.36), residues: 200 sheet: -0.28 (0.40), residues: 145 loop : -0.55 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 195 TYR 0.026 0.002 TYR A 490 PHE 0.023 0.002 PHE A 67 TRP 0.024 0.002 TRP A 131 HIS 0.008 0.001 HIS A 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 6181) covalent geometry : angle 0.75107 / 0.38 ( 8347) hydrogen bonds : bond 0.04898 / 3.24 ( 266) hydrogen bonds : angle 6.18424 / 4.26 ( 756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.9666 (mm110) cc_final: 0.9446 (tp-100) REVERT: A 44 LYS cc_start: 0.8770 (mmpt) cc_final: 0.8497 (mmmt) REVERT: A 97 TYR cc_start: 0.9055 (m-80) cc_final: 0.8703 (m-80) REVERT: A 107 HIS cc_start: 0.9552 (OUTLIER) cc_final: 0.9243 (p-80) REVERT: A 118 TYR cc_start: 0.9425 (t80) cc_final: 0.8906 (t80) REVERT: A 161 LEU cc_start: 0.9357 (tp) cc_final: 0.8636 (tp) REVERT: A 174 ASP cc_start: 0.9024 (t0) cc_final: 0.8643 (t0) REVERT: A 419 ILE cc_start: 0.9773 (mt) cc_final: 0.9522 (pt) REVERT: A 467 LEU cc_start: 0.9586 (mp) cc_final: 0.9353 (mt) REVERT: A 481 PHE cc_start: 0.9508 (t80) cc_final: 0.9073 (t80) REVERT: A 496 GLN cc_start: 0.9446 (tm-30) cc_final: 0.8629 (tm-30) REVERT: A 521 TYR cc_start: 0.9533 (m-80) cc_final: 0.8839 (m-80) REVERT: A 522 ARG cc_start: 0.9317 (tpp80) cc_final: 0.9078 (mmm-85) REVERT: A 673 LYS cc_start: 0.8863 (ptpt) cc_final: 0.8660 (pptt) REVERT: A 737 MET cc_start: 0.9244 (mmm) cc_final: 0.8770 (mmm) REVERT: A 740 MET cc_start: 0.9522 (mtm) cc_final: 0.8834 (mtm) REVERT: A 744 PHE cc_start: 0.9354 (t80) cc_final: 0.8882 (t80) REVERT: A 748 MET cc_start: 0.9208 (mmm) cc_final: 0.9000 (mmm) outliers start: 14 outliers final: 7 residues processed: 168 average time/residue: 0.0964 time to fit residues: 20.3908 Evaluate side-chains 140 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 107 HIS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 677 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 0.0570 chunk 16 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 213 ASN ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 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 = 0.3495 r_free = 0.3495 target = 0.069806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.049701 restraints weight = 25162.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.051497 restraints weight = 16563.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.052775 restraints weight = 12276.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.053614 restraints weight = 9846.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.054363 restraints weight = 8472.593| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6181 Z= 0.185 Angle : 0.689 8.042 8347 Z= 0.354 Chirality : 0.044 0.165 909 Planarity : 0.005 0.044 1067 Dihedral : 4.603 20.671 811 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.66 % Favored : 96.07 % Rotamer: Outliers : 2.57 % Allowed : 15.86 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.34 (0.30), residues: 737 helix: 0.69 (0.36), residues: 203 sheet: -0.48 (0.36), residues: 160 loop : -0.53 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 195 TYR 0.028 0.002 TYR A 9 PHE 0.025 0.002 PHE A 353 TRP 0.012 0.002 TRP A 131 HIS 0.014 0.001 HIS A 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 ( 6181) covalent geometry : angle 0.68897 / 0.35 ( 8347) hydrogen bonds : bond 0.04368 / 2.85 ( 266) hydrogen bonds : angle 6.13773 / 4.19 ( 756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.254 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 43 GLN cc_start: 0.9681 (mm110) cc_final: 0.9392 (tp-100) REVERT: A 44 LYS cc_start: 0.8816 (mmpt) cc_final: 0.8459 (mmpt) REVERT: A 76 MET cc_start: 0.7737 (tpp) cc_final: 0.7532 (tpp) REVERT: A 97 TYR cc_start: 0.9095 (m-80) cc_final: 0.8797 (m-80) REVERT: A 99 ILE cc_start: 0.9133 (tt) cc_final: 0.8854 (mp) REVERT: A 118 TYR cc_start: 0.9389 (t80) cc_final: 0.8854 (t80) REVERT: A 160 LYS cc_start: 0.9434 (tppt) cc_final: 0.9005 (tptp) REVERT: A 161 LEU cc_start: 0.9194 (tp) cc_final: 0.8364 (tp) REVERT: A 172 THR cc_start: 0.9736 (m) cc_final: 0.9347 (p) REVERT: A 481 PHE cc_start: 0.9553 (t80) cc_final: 0.9178 (t80) REVERT: A 496 GLN cc_start: 0.9379 (tm-30) cc_final: 0.9125 (tm-30) REVERT: A 521 TYR cc_start: 0.9493 (m-80) cc_final: 0.8806 (m-80) REVERT: A 522 ARG cc_start: 0.9283 (tpp80) cc_final: 0.8843 (mmm160) REVERT: A 531 PHE cc_start: 0.9528 (t80) cc_final: 0.9183 (t80) REVERT: A 706 GLU cc_start: 0.8189 (mp0) cc_final: 0.7746 (mp0) REVERT: A 740 MET cc_start: 0.9515 (mtm) cc_final: 0.9051 (mtm) outliers start: 17 outliers final: 14 residues processed: 151 average time/residue: 0.0945 time to fit residues: 18.4005 Evaluate side-chains 134 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 679 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 2 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS A 213 ASN A 445 GLN A 447 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.069738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.048884 restraints weight = 26356.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.050704 restraints weight = 17327.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.052010 restraints weight = 12924.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.052952 restraints weight = 10436.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.053611 restraints weight = 8958.707| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6181 Z= 0.154 Angle : 0.672 9.153 8347 Z= 0.340 Chirality : 0.045 0.189 909 Planarity : 0.005 0.047 1067 Dihedral : 4.594 19.679 811 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.99 % Favored : 96.61 % Rotamer: Outliers : 3.17 % Allowed : 17.37 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.42 (0.30), residues: 737 helix: 0.52 (0.36), residues: 209 sheet: -0.60 (0.38), residues: 152 loop : -0.51 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 195 TYR 0.029 0.002 TYR A 9 PHE 0.016 0.002 PHE A 429 TRP 0.011 0.001 TRP A 347 HIS 0.008 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 6181) covalent geometry : angle 0.67152 / 0.34 ( 8347) hydrogen bonds : bond 0.04103 / 2.67 ( 266) hydrogen bonds : angle 6.02266 / 4.10 ( 756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.9662 (mm110) cc_final: 0.9439 (tp-100) REVERT: A 44 LYS cc_start: 0.8834 (mmpt) cc_final: 0.8522 (mmmt) REVERT: A 76 MET cc_start: 0.7830 (tpp) cc_final: 0.7525 (tpp) REVERT: A 97 TYR cc_start: 0.9150 (m-80) cc_final: 0.8827 (m-80) REVERT: A 99 ILE cc_start: 0.9118 (tt) cc_final: 0.8846 (mp) REVERT: A 113 TYR cc_start: 0.9397 (t80) cc_final: 0.8342 (t80) REVERT: A 160 LYS cc_start: 0.9424 (tppt) cc_final: 0.9020 (tptp) REVERT: A 161 LEU cc_start: 0.9115 (tp) cc_final: 0.7813 (tp) REVERT: A 172 THR cc_start: 0.9690 (m) cc_final: 0.9426 (p) REVERT: A 205 ARG cc_start: 0.8290 (mmm160) cc_final: 0.7694 (mtm110) REVERT: A 273 ARG cc_start: 0.8945 (ptt-90) cc_final: 0.8705 (ptt-90) REVERT: A 481 PHE cc_start: 0.9542 (t80) cc_final: 0.9189 (t80) REVERT: A 496 GLN cc_start: 0.9352 (tm-30) cc_final: 0.9072 (tm-30) REVERT: A 521 TYR cc_start: 0.9506 (m-80) cc_final: 0.8867 (m-80) REVERT: A 531 PHE cc_start: 0.9523 (t80) cc_final: 0.9250 (t80) REVERT: A 537 TYR cc_start: 0.9284 (m-80) cc_final: 0.8344 (m-80) REVERT: A 688 TYR cc_start: 0.9057 (p90) cc_final: 0.8645 (p90) REVERT: A 706 GLU cc_start: 0.8237 (mp0) cc_final: 0.7866 (mp0) REVERT: A 737 MET cc_start: 0.9290 (mmm) cc_final: 0.8789 (mmm) REVERT: A 740 MET cc_start: 0.9462 (mtm) cc_final: 0.8609 (mtm) outliers start: 21 outliers final: 15 residues processed: 143 average time/residue: 0.0829 time to fit residues: 15.4761 Evaluate side-chains 136 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 679 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.064525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.045060 restraints weight = 26691.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.046709 restraints weight = 17714.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.047938 restraints weight = 13236.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.048798 restraints weight = 10649.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.049404 restraints weight = 9099.170| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6181 Z= 0.256 Angle : 0.721 9.128 8347 Z= 0.371 Chirality : 0.045 0.194 909 Planarity : 0.005 0.050 1067 Dihedral : 4.824 22.701 811 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.48 % Favored : 95.39 % Rotamer: Outliers : 3.63 % Allowed : 17.07 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.23 (0.30), residues: 737 helix: 0.69 (0.36), residues: 209 sheet: -0.34 (0.36), residues: 178 loop : -0.47 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 195 TYR 0.036 0.002 TYR A 9 PHE 0.049 0.003 PHE A 744 TRP 0.007 0.001 TRP A 347 HIS 0.009 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.26 ( 6181) covalent geometry : angle 0.72111 / 0.37 ( 8347) hydrogen bonds : bond 0.04307 / 2.74 ( 266) hydrogen bonds : angle 6.22735 / 4.26 ( 756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.9438 (p90) cc_final: 0.8904 (p90) REVERT: A 43 GLN cc_start: 0.9670 (mm110) cc_final: 0.9440 (tp-100) REVERT: A 44 LYS cc_start: 0.8842 (mmpt) cc_final: 0.8515 (mmmt) REVERT: A 76 MET cc_start: 0.7943 (tpp) cc_final: 0.6346 (tpp) REVERT: A 91 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8977 (mmtt) REVERT: A 97 TYR cc_start: 0.9145 (m-80) cc_final: 0.8291 (m-80) REVERT: A 113 TYR cc_start: 0.9362 (t80) cc_final: 0.8817 (t80) REVERT: A 160 LYS cc_start: 0.9469 (tppt) cc_final: 0.9249 (tptm) REVERT: A 161 LEU cc_start: 0.9122 (tp) cc_final: 0.8225 (tp) REVERT: A 205 ARG cc_start: 0.8306 (mmm160) cc_final: 0.7686 (mtm110) REVERT: A 294 GLU cc_start: 0.9316 (pm20) cc_final: 0.9094 (pm20) REVERT: A 414 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8881 (p0) REVERT: A 481 PHE cc_start: 0.9582 (t80) cc_final: 0.9254 (t80) REVERT: A 496 GLN cc_start: 0.9252 (tm-30) cc_final: 0.8568 (tm-30) REVERT: A 521 TYR cc_start: 0.9503 (m-80) cc_final: 0.8956 (m-80) REVERT: A 531 PHE cc_start: 0.9551 (t80) cc_final: 0.9260 (t80) REVERT: A 541 GLU cc_start: 0.9275 (pt0) cc_final: 0.8837 (pp20) REVERT: A 688 TYR cc_start: 0.9096 (p90) cc_final: 0.8638 (p90) REVERT: A 691 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8721 (pp) REVERT: A 706 GLU cc_start: 0.8290 (mp0) cc_final: 0.7920 (mp0) REVERT: A 729 MET cc_start: 0.8800 (tpt) cc_final: 0.8575 (tpt) REVERT: A 737 MET cc_start: 0.9330 (mmm) cc_final: 0.8782 (mmm) REVERT: A 740 MET cc_start: 0.9517 (mtm) cc_final: 0.8651 (mpp) REVERT: A 741 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8687 (tm-30) outliers start: 24 outliers final: 16 residues processed: 136 average time/residue: 0.0830 time to fit residues: 14.9383 Evaluate side-chains 129 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 582 GLU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 40 optimal weight: 0.4980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** 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 = 0.3441 r_free = 0.3441 target = 0.066500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047323 restraints weight = 25773.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048963 restraints weight = 17022.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.050180 restraints weight = 12759.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.051052 restraints weight = 10267.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.051687 restraints weight = 8775.862| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6181 Z= 0.159 Angle : 0.711 14.173 8347 Z= 0.350 Chirality : 0.045 0.225 909 Planarity : 0.004 0.047 1067 Dihedral : 4.599 18.515 811 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.80 % Favored : 96.07 % Rotamer: Outliers : 2.87 % Allowed : 20.69 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.23 (0.31), residues: 737 helix: 0.64 (0.35), residues: 215 sheet: -0.32 (0.36), residues: 183 loop : -0.45 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 195 TYR 0.018 0.001 TYR A 9 PHE 0.045 0.002 PHE A 744 TRP 0.013 0.001 TRP A 347 HIS 0.008 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 6181) covalent geometry : angle 0.71085 / 0.35 ( 8347) hydrogen bonds : bond 0.03910 / 2.56 ( 266) hydrogen bonds : angle 6.05203 / 4.13 ( 756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.9371 (p90) cc_final: 0.8870 (p90) REVERT: A 43 GLN cc_start: 0.9671 (mm110) cc_final: 0.9442 (tp-100) REVERT: A 44 LYS cc_start: 0.8827 (mmpt) cc_final: 0.8497 (mmmt) REVERT: A 76 MET cc_start: 0.7942 (tpp) cc_final: 0.6335 (tpp) REVERT: A 91 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8992 (mmtt) REVERT: A 97 TYR cc_start: 0.9139 (m-80) cc_final: 0.8304 (m-80) REVERT: A 113 TYR cc_start: 0.9345 (t80) cc_final: 0.8495 (t80) REVERT: A 160 LYS cc_start: 0.9355 (tppt) cc_final: 0.9079 (tptp) REVERT: A 161 LEU cc_start: 0.9115 (tp) cc_final: 0.7765 (tp) REVERT: A 275 MET cc_start: 0.6667 (ptp) cc_final: 0.5907 (ptp) REVERT: A 294 GLU cc_start: 0.9286 (pm20) cc_final: 0.9054 (pm20) REVERT: A 414 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8869 (p0) REVERT: A 481 PHE cc_start: 0.9575 (t80) cc_final: 0.9225 (t80) REVERT: A 496 GLN cc_start: 0.9339 (tm-30) cc_final: 0.8473 (tm-30) REVERT: A 521 TYR cc_start: 0.9499 (m-80) cc_final: 0.8922 (m-80) REVERT: A 531 PHE cc_start: 0.9530 (t80) cc_final: 0.9259 (t80) REVERT: A 541 GLU cc_start: 0.9263 (pt0) cc_final: 0.8837 (pp20) REVERT: A 688 TYR cc_start: 0.9077 (p90) cc_final: 0.8697 (p90) REVERT: A 706 GLU cc_start: 0.8233 (mp0) cc_final: 0.7835 (mp0) REVERT: A 737 MET cc_start: 0.9345 (mmm) cc_final: 0.8786 (mmm) REVERT: A 740 MET cc_start: 0.9523 (mtm) cc_final: 0.8618 (mpp) REVERT: A 741 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8689 (tm-30) outliers start: 19 outliers final: 14 residues processed: 128 average time/residue: 0.0803 time to fit residues: 13.7500 Evaluate side-chains 126 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 61 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 26 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.068089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.048801 restraints weight = 25565.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050481 restraints weight = 16835.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.051743 restraints weight = 12538.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.052650 restraints weight = 10050.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053215 restraints weight = 8544.150| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6181 Z= 0.134 Angle : 0.715 15.182 8347 Z= 0.349 Chirality : 0.046 0.222 909 Planarity : 0.004 0.049 1067 Dihedral : 4.533 19.055 811 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.07 % Favored : 95.66 % Rotamer: Outliers : 3.02 % Allowed : 21.30 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.16 (0.31), residues: 737 helix: 0.77 (0.36), residues: 215 sheet: -0.29 (0.37), residues: 174 loop : -0.45 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 195 TYR 0.020 0.001 TYR A 490 PHE 0.019 0.002 PHE A 411 TRP 0.010 0.001 TRP A 347 HIS 0.007 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 6181) covalent geometry : angle 0.71528 / 0.35 ( 8347) hydrogen bonds : bond 0.03792 / 2.49 ( 266) hydrogen bonds : angle 5.88842 / 4.01 ( 756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.9364 (p90) cc_final: 0.8903 (p90) REVERT: A 43 GLN cc_start: 0.9663 (mm110) cc_final: 0.9432 (tp-100) REVERT: A 44 LYS cc_start: 0.8815 (mmpt) cc_final: 0.8477 (mmmt) REVERT: A 76 MET cc_start: 0.7908 (tpp) cc_final: 0.6242 (tpp) REVERT: A 91 LYS cc_start: 0.9340 (pttm) cc_final: 0.9030 (mmtt) REVERT: A 97 TYR cc_start: 0.9130 (m-80) cc_final: 0.8289 (m-80) REVERT: A 113 TYR cc_start: 0.9403 (t80) cc_final: 0.8380 (t80) REVERT: A 144 MET cc_start: 0.8361 (ptp) cc_final: 0.7995 (ptp) REVERT: A 160 LYS cc_start: 0.9370 (tppt) cc_final: 0.9169 (tptp) REVERT: A 161 LEU cc_start: 0.8993 (tp) cc_final: 0.7633 (tp) REVERT: A 275 MET cc_start: 0.6608 (ptp) cc_final: 0.5881 (ptp) REVERT: A 294 GLU cc_start: 0.9257 (pm20) cc_final: 0.9037 (pm20) REVERT: A 414 ASN cc_start: 0.9180 (OUTLIER) cc_final: 0.8953 (p0) REVERT: A 481 PHE cc_start: 0.9563 (t80) cc_final: 0.9267 (t80) REVERT: A 496 GLN cc_start: 0.9386 (tm-30) cc_final: 0.8650 (tm-30) REVERT: A 521 TYR cc_start: 0.9502 (m-80) cc_final: 0.8923 (m-80) REVERT: A 531 PHE cc_start: 0.9492 (t80) cc_final: 0.9252 (t80) REVERT: A 541 GLU cc_start: 0.9251 (pt0) cc_final: 0.8824 (pp20) REVERT: A 673 LYS cc_start: 0.8733 (ptpt) cc_final: 0.8528 (ptpt) REVERT: A 691 LEU cc_start: 0.9268 (mt) cc_final: 0.8633 (pp) REVERT: A 706 GLU cc_start: 0.8321 (mp0) cc_final: 0.7969 (mp0) REVERT: A 737 MET cc_start: 0.9367 (mmm) cc_final: 0.8793 (mmm) REVERT: A 740 MET cc_start: 0.9527 (mtm) cc_final: 0.8623 (mpp) REVERT: A 741 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8618 (tm-30) outliers start: 20 outliers final: 14 residues processed: 131 average time/residue: 0.0809 time to fit residues: 14.0318 Evaluate side-chains 133 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 749 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 23 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** 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 = 0.3442 r_free = 0.3442 target = 0.066360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.047504 restraints weight = 26230.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.049212 restraints weight = 16988.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.050420 restraints weight = 12541.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.051305 restraints weight = 10061.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.051922 restraints weight = 8534.254| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6181 Z= 0.152 Angle : 0.714 15.205 8347 Z= 0.349 Chirality : 0.046 0.234 909 Planarity : 0.004 0.049 1067 Dihedral : 4.503 19.349 811 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.21 % Favored : 95.66 % Rotamer: Outliers : 3.32 % Allowed : 21.90 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.13 (0.31), residues: 737 helix: 0.81 (0.36), residues: 215 sheet: -0.32 (0.36), residues: 182 loop : -0.43 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 195 TYR 0.026 0.002 TYR A 9 PHE 0.023 0.002 PHE A 429 TRP 0.004 0.001 TRP A 549 HIS 0.009 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 6181) covalent geometry : angle 0.71420 / 0.35 ( 8347) hydrogen bonds : bond 0.03791 / 2.48 ( 266) hydrogen bonds : angle 5.90014 / 4.03 ( 756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLN cc_start: 0.9667 (mm110) cc_final: 0.9438 (tp-100) REVERT: A 44 LYS cc_start: 0.8843 (mmpt) cc_final: 0.8502 (mmmt) REVERT: A 76 MET cc_start: 0.7877 (tpp) cc_final: 0.6145 (tpp) REVERT: A 91 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.9041 (mmpt) REVERT: A 97 TYR cc_start: 0.9129 (m-80) cc_final: 0.8735 (m-80) REVERT: A 113 TYR cc_start: 0.9424 (t80) cc_final: 0.8843 (t80) REVERT: A 144 MET cc_start: 0.8493 (ptp) cc_final: 0.8111 (ptp) REVERT: A 161 LEU cc_start: 0.9007 (tp) cc_final: 0.7905 (tp) REVERT: A 275 MET cc_start: 0.6701 (ptp) cc_final: 0.5983 (ptp) REVERT: A 294 GLU cc_start: 0.9290 (pm20) cc_final: 0.9078 (pm20) REVERT: A 357 ARG cc_start: 0.9582 (mmm160) cc_final: 0.9317 (mmm160) REVERT: A 414 ASN cc_start: 0.9200 (OUTLIER) cc_final: 0.8979 (p0) REVERT: A 481 PHE cc_start: 0.9587 (t80) cc_final: 0.9252 (t80) REVERT: A 496 GLN cc_start: 0.9405 (tm-30) cc_final: 0.8647 (tm-30) REVERT: A 521 TYR cc_start: 0.9518 (m-80) cc_final: 0.8964 (m-80) REVERT: A 531 PHE cc_start: 0.9517 (t80) cc_final: 0.9283 (t80) REVERT: A 541 GLU cc_start: 0.9263 (pt0) cc_final: 0.8824 (pp20) REVERT: A 688 TYR cc_start: 0.9064 (p90) cc_final: 0.8651 (p90) REVERT: A 691 LEU cc_start: 0.9266 (mt) cc_final: 0.8638 (pp) REVERT: A 706 GLU cc_start: 0.8296 (mp0) cc_final: 0.7923 (mp0) REVERT: A 737 MET cc_start: 0.9365 (mmm) cc_final: 0.8798 (mmm) REVERT: A 740 MET cc_start: 0.9542 (mtm) cc_final: 0.8629 (mpp) REVERT: A 741 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8689 (tm-30) outliers start: 22 outliers final: 16 residues processed: 132 average time/residue: 0.0825 time to fit residues: 14.4485 Evaluate side-chains 131 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 679 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 0.0770 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** 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 = 0.3489 r_free = 0.3489 target = 0.069218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.048872 restraints weight = 26835.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.050684 restraints weight = 17653.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.051944 restraints weight = 13148.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.052825 restraints weight = 10662.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.053452 restraints weight = 9162.575| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 6181 Z= 0.132 Angle : 0.732 15.219 8347 Z= 0.355 Chirality : 0.046 0.167 909 Planarity : 0.004 0.048 1067 Dihedral : 4.409 19.986 811 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.53 % Favored : 96.07 % Rotamer: Outliers : 2.87 % Allowed : 22.05 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.22 (0.31), residues: 737 helix: 0.73 (0.36), residues: 215 sheet: -0.33 (0.36), residues: 175 loop : -0.50 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 680 TYR 0.019 0.001 TYR A 490 PHE 0.020 0.002 PHE A 411 TRP 0.006 0.001 TRP A 131 HIS 0.008 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 6181) covalent geometry : angle 0.73165 / 0.36 ( 8347) hydrogen bonds : bond 0.03706 / 2.47 ( 266) hydrogen bonds : angle 5.93853 / 4.10 ( 756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.9209 (p90) cc_final: 0.8912 (p90) REVERT: A 43 GLN cc_start: 0.9649 (mm110) cc_final: 0.9440 (tp-100) REVERT: A 44 LYS cc_start: 0.8845 (mmpt) cc_final: 0.8513 (mmmt) REVERT: A 76 MET cc_start: 0.7947 (tpp) cc_final: 0.6262 (tpp) REVERT: A 91 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9078 (mmpt) REVERT: A 97 TYR cc_start: 0.9150 (m-80) cc_final: 0.8408 (m-80) REVERT: A 113 TYR cc_start: 0.9397 (t80) cc_final: 0.8787 (t80) REVERT: A 118 TYR cc_start: 0.9422 (t80) cc_final: 0.8866 (t80) REVERT: A 144 MET cc_start: 0.8513 (ptp) cc_final: 0.8154 (ptp) REVERT: A 161 LEU cc_start: 0.8908 (tp) cc_final: 0.7828 (tp) REVERT: A 275 MET cc_start: 0.6662 (ptp) cc_final: 0.5972 (ptp) REVERT: A 294 GLU cc_start: 0.9323 (pm20) cc_final: 0.9119 (pm20) REVERT: A 481 PHE cc_start: 0.9550 (t80) cc_final: 0.9191 (t80) REVERT: A 496 GLN cc_start: 0.9410 (tm-30) cc_final: 0.8618 (tm-30) REVERT: A 521 TYR cc_start: 0.9512 (m-80) cc_final: 0.8915 (m-80) REVERT: A 541 GLU cc_start: 0.9230 (pt0) cc_final: 0.8795 (pp20) REVERT: A 688 TYR cc_start: 0.9059 (p90) cc_final: 0.8653 (p90) REVERT: A 691 LEU cc_start: 0.9187 (mt) cc_final: 0.8541 (pp) REVERT: A 706 GLU cc_start: 0.8283 (mp0) cc_final: 0.7940 (mp0) REVERT: A 737 MET cc_start: 0.9323 (mmm) cc_final: 0.8800 (mmm) REVERT: A 740 MET cc_start: 0.9517 (mtm) cc_final: 0.8544 (mpp) REVERT: A 741 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8645 (tm-30) outliers start: 19 outliers final: 15 residues processed: 133 average time/residue: 0.0808 time to fit residues: 14.4479 Evaluate side-chains 136 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 679 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 48 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 8 optimal weight: 8.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** 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 = 0.3453 r_free = 0.3453 target = 0.066896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.046947 restraints weight = 27867.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.048693 restraints weight = 17982.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.049932 restraints weight = 13307.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.050803 restraints weight = 10736.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.051430 restraints weight = 9193.638| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6181 Z= 0.168 Angle : 0.776 14.780 8347 Z= 0.378 Chirality : 0.047 0.245 909 Planarity : 0.004 0.051 1067 Dihedral : 4.489 19.063 811 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.48 % Favored : 95.12 % Rotamer: Outliers : 2.42 % Allowed : 23.56 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.32 (0.31), residues: 737 helix: 0.55 (0.35), residues: 214 sheet: -0.45 (0.35), residues: 183 loop : -0.44 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 375 TYR 0.014 0.002 TYR A 9 PHE 0.019 0.002 PHE A 429 TRP 0.008 0.001 TRP A 549 HIS 0.010 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 6181) covalent geometry : angle 0.77636 / 0.38 ( 8347) hydrogen bonds : bond 0.04031 / 2.63 ( 266) hydrogen bonds : angle 6.02951 / 4.18 ( 756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.9221 (p90) cc_final: 0.8925 (p90) REVERT: A 43 GLN cc_start: 0.9655 (mm110) cc_final: 0.9450 (tp-100) REVERT: A 44 LYS cc_start: 0.8861 (mmpt) cc_final: 0.8553 (mmmt) REVERT: A 76 MET cc_start: 0.8050 (tpp) cc_final: 0.6398 (tpp) REVERT: A 91 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9074 (mmpt) REVERT: A 97 TYR cc_start: 0.9115 (m-80) cc_final: 0.8251 (m-80) REVERT: A 113 TYR cc_start: 0.9372 (t80) cc_final: 0.8696 (t80) REVERT: A 114 LYS cc_start: 0.9694 (mmtm) cc_final: 0.9369 (mppt) REVERT: A 118 TYR cc_start: 0.9407 (t80) cc_final: 0.8863 (t80) REVERT: A 144 MET cc_start: 0.8583 (ptp) cc_final: 0.8204 (ptp) REVERT: A 161 LEU cc_start: 0.8957 (tp) cc_final: 0.7866 (tp) REVERT: A 275 MET cc_start: 0.6876 (ptp) cc_final: 0.6654 (ptp) REVERT: A 357 ARG cc_start: 0.9562 (mmm160) cc_final: 0.9327 (mmm160) REVERT: A 481 PHE cc_start: 0.9568 (t80) cc_final: 0.9210 (t80) REVERT: A 496 GLN cc_start: 0.9329 (tm-30) cc_final: 0.8570 (tm-30) REVERT: A 521 TYR cc_start: 0.9504 (m-80) cc_final: 0.8937 (m-80) REVERT: A 541 GLU cc_start: 0.9247 (pt0) cc_final: 0.8797 (pp20) REVERT: A 688 TYR cc_start: 0.9086 (p90) cc_final: 0.8709 (p90) REVERT: A 691 LEU cc_start: 0.9210 (mt) cc_final: 0.8561 (pp) REVERT: A 706 GLU cc_start: 0.8291 (mp0) cc_final: 0.7943 (mp0) REVERT: A 737 MET cc_start: 0.9349 (mmm) cc_final: 0.8778 (mmm) REVERT: A 740 MET cc_start: 0.9522 (mtm) cc_final: 0.8602 (mpp) REVERT: A 741 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8629 (tm-30) outliers start: 16 outliers final: 15 residues processed: 123 average time/residue: 0.0766 time to fit residues: 12.6874 Evaluate side-chains 127 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 679 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 0.0770 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** 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 = 0.3500 r_free = 0.3500 target = 0.069286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.048834 restraints weight = 27049.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.050677 restraints weight = 17671.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051941 restraints weight = 13160.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.052820 restraints weight = 10680.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.053460 restraints weight = 9188.158| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6181 Z= 0.140 Angle : 0.804 15.371 8347 Z= 0.392 Chirality : 0.048 0.219 909 Planarity : 0.004 0.049 1067 Dihedral : 4.466 21.765 811 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.93 % Favored : 95.66 % Rotamer: Outliers : 2.42 % Allowed : 23.72 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.50 (0.31), residues: 737 helix: 0.42 (0.35), residues: 215 sheet: -0.58 (0.36), residues: 179 loop : -0.55 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.013 0.001 TYR A 9 PHE 0.025 0.002 PHE A 429 TRP 0.006 0.001 TRP A 131 HIS 0.009 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 6181) covalent geometry : angle 0.80410 / 0.39 ( 8347) hydrogen bonds : bond 0.04142 / 2.79 ( 266) hydrogen bonds : angle 6.01216 / 4.13 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1327.96 seconds wall clock time: 23 minutes 45.51 seconds (1425.51 seconds total)