Starting phenix.real_space_refine on Thu Mar 13 12:21:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vjz_21221/03_2025/6vjz_21221.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vjz_21221/03_2025/6vjz_21221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vjz_21221/03_2025/6vjz_21221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vjz_21221/03_2025/6vjz_21221.map" model { file = "/net/cci-nas-00/data/ceres_data/6vjz_21221/03_2025/6vjz_21221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vjz_21221/03_2025/6vjz_21221.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 43 5.16 5 C 5875 2.51 5 N 1477 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8996 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1355 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "B" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2343 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4923 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 20, 'TRANS': 582} Chain breaks: 4 Chain: "D" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 375 Classifications: {'peptide': 45} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 40} Time building chain proxies: 5.35, per 1000 atoms: 0.59 Number of scatterers: 8996 At special positions: 0 Unit cell: (103.95, 101.25, 151.2, 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 43 16.00 O 1601 8.00 N 1477 7.00 C 5875 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'C' and resid 13 through 32 Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.969A pdb=" N VAL C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 41' Processing helix chain 'C' and resid 43 through 51 Processing helix chain 'C' and resid 52 through 62 removed outlier: 3.752A pdb=" N LEU C 56 " --> pdb=" O GLN C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 86 Processing helix chain 'C' and resid 90 through 113 Processing helix chain 'C' and resid 117 through 134 removed outlier: 3.692A pdb=" N LEU C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 166 removed outlier: 4.099A pdb=" N ILE C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 192 Proline residue: C 178 - end of helix Processing helix chain 'B' and resid 3 through 31 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 44 through 72 Processing helix chain 'B' and resid 75 through 98 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 99 through 100 No H-bonds generated for 'chain 'B' and resid 99 through 100' Processing helix chain 'B' and resid 101 through 104 Processing helix chain 'B' and resid 105 through 135 Processing helix chain 'B' and resid 143 through 175 Processing helix chain 'B' and resid 179 through 220 removed outlier: 3.888A pdb=" N THR B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 294 removed outlier: 3.652A pdb=" N TYR B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 297 through 324 Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.643A pdb=" N GLU A 46 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 80 Processing helix chain 'A' and resid 83 through 100 removed outlier: 3.610A pdb=" N PHE A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 123 through 139 removed outlier: 3.655A pdb=" N ALA A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.720A pdb=" N GLY A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 Processing helix chain 'A' and resid 206 through 223 removed outlier: 3.902A pdb=" N SER A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 315 through 331 removed outlier: 4.230A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 removed outlier: 4.025A pdb=" N ALA A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 364 through 383 removed outlier: 3.842A pdb=" N TYR A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 407 removed outlier: 4.088A pdb=" N ARG A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 426 Processing helix chain 'A' and resid 429 through 442 removed outlier: 3.907A pdb=" N ALA A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LYS A 442 " --> pdb=" O MET A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 462 through 465 removed outlier: 3.693A pdb=" N LYS A 465 " --> pdb=" O PRO A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 468 through 480 Processing helix chain 'A' and resid 481 through 495 removed outlier: 3.866A pdb=" N ILE A 485 " --> pdb=" O PHE A 481 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 517 removed outlier: 3.687A pdb=" N THR A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 533 removed outlier: 4.074A pdb=" N THR A 526 " --> pdb=" O PRO A 522 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 548 removed outlier: 3.937A pdb=" N ALA A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.661A pdb=" N GLY A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 610 removed outlier: 3.506A pdb=" N VAL A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.608A pdb=" N HIS A 640 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 665 through 686 removed outlier: 3.779A pdb=" N THR A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 753 Processing helix chain 'D' and resid 763 through 777 removed outlier: 3.579A pdb=" N VAL D 777 " --> pdb=" O VAL D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 789 removed outlier: 4.274A pdb=" N ASP D 788 " --> pdb=" O LYS D 784 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP D 789 " --> pdb=" O GLU D 785 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1890 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: 2.35 Time building geometry restraints manager: 2.99 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: 2775 1.34 - 1.46: 2192 1.46 - 1.58: 4177 1.58 - 1.70: 0 1.70 - 1.81: 77 Bond restraints: 9221 Sorted by residual: bond pdb=" N HIS B 101 " pdb=" CA HIS B 101 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.14e-02 7.69e+03 7.54e+00 bond pdb=" C ALA A 521 " pdb=" N PRO A 522 " ideal model delta sigma weight residual 1.337 1.305 0.033 1.24e-02 6.50e+03 6.88e+00 bond pdb=" CE1 HIS B 101 " pdb=" NE2 HIS B 101 " ideal model delta sigma weight residual 1.321 1.339 -0.018 1.00e-02 1.00e+04 3.14e+00 bond pdb=" C HIS B 101 " pdb=" O HIS B 101 " ideal model delta sigma weight residual 1.234 1.250 -0.016 1.07e-02 8.73e+03 2.29e+00 bond pdb=" CB VAL A 658 " pdb=" CG1 VAL A 658 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.83e+00 ... (remaining 9216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 11989 1.87 - 3.74: 435 3.74 - 5.61: 52 5.61 - 7.48: 10 7.48 - 9.34: 5 Bond angle restraints: 12491 Sorted by residual: angle pdb=" N GLY C 64 " pdb=" CA GLY C 64 " pdb=" C GLY C 64 " ideal model delta sigma weight residual 114.16 104.82 9.34 2.00e+00 2.50e-01 2.18e+01 angle pdb=" C PRO D 757 " pdb=" N ASP D 758 " pdb=" CA ASP D 758 " ideal model delta sigma weight residual 121.70 129.64 -7.94 1.80e+00 3.09e-01 1.95e+01 angle pdb=" CA TYR B 104 " pdb=" C TYR B 104 " pdb=" N PHE B 105 " ideal model delta sigma weight residual 114.59 120.13 -5.54 1.48e+00 4.57e-01 1.40e+01 angle pdb=" C TYR B 104 " pdb=" N PHE B 105 " pdb=" CA PHE B 105 " ideal model delta sigma weight residual 122.42 116.63 5.79 1.55e+00 4.16e-01 1.40e+01 angle pdb=" N GLY A 253 " pdb=" CA GLY A 253 " pdb=" C GLY A 253 " ideal model delta sigma weight residual 112.48 116.81 -4.33 1.21e+00 6.83e-01 1.28e+01 ... (remaining 12486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 4806 16.75 - 33.51: 518 33.51 - 50.26: 93 50.26 - 67.02: 18 67.02 - 83.77: 12 Dihedral angle restraints: 5447 sinusoidal: 2189 harmonic: 3258 Sorted by residual: dihedral pdb=" CA TYR C 63 " pdb=" C TYR C 63 " pdb=" N GLY C 64 " pdb=" CA GLY C 64 " ideal model delta harmonic sigma weight residual -180.00 -151.24 -28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ASN A 516 " pdb=" C ASN A 516 " pdb=" N GLU A 517 " pdb=" CA GLU A 517 " ideal model delta harmonic sigma weight residual 180.00 153.94 26.06 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA SER A 245 " pdb=" C SER A 245 " pdb=" N ASP A 246 " pdb=" CA ASP A 246 " ideal model delta harmonic sigma weight residual 180.00 154.07 25.93 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 5444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1199 0.065 - 0.131: 179 0.131 - 0.196: 9 0.196 - 0.262: 0 0.262 - 0.327: 1 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA LEU A 252 " pdb=" N LEU A 252 " pdb=" C LEU A 252 " pdb=" CB LEU A 252 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB VAL D 777 " pdb=" CA VAL D 777 " pdb=" CG1 VAL D 777 " pdb=" CG2 VAL D 777 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA THR D 778 " pdb=" N THR D 778 " pdb=" C THR D 778 " pdb=" CB THR D 778 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.52e-01 ... (remaining 1385 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 100 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.23e+00 pdb=" C PHE B 100 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE B 100 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS B 101 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 758 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO D 759 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 759 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 759 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 305 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C TRP B 305 " 0.029 2.00e-02 2.50e+03 pdb=" O TRP B 305 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP B 306 " -0.010 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1090 2.74 - 3.28: 10487 3.28 - 3.82: 14944 3.82 - 4.36: 17123 4.36 - 4.90: 26922 Nonbonded interactions: 70566 Sorted by model distance: nonbonded pdb=" O TYR A 107 " pdb=" OG SER A 110 " model vdw 2.195 3.040 nonbonded pdb=" O GLU A 463 " pdb=" NZ LYS A 465 " model vdw 2.204 3.120 nonbonded pdb=" O PHE B 95 " pdb=" OG SER B 98 " model vdw 2.214 3.040 nonbonded pdb=" O GLN B 312 " pdb=" OG1 THR B 315 " model vdw 2.222 3.040 nonbonded pdb=" O LEU B 118 " pdb=" ND1 HIS B 122 " model vdw 2.223 3.120 ... (remaining 70561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 22.720 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9221 Z= 0.409 Angle : 0.832 9.345 12491 Z= 0.485 Chirality : 0.046 0.327 1388 Planarity : 0.005 0.059 1546 Dihedral : 14.502 83.769 3343 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.15 % Favored : 93.76 % Rotamer: Outliers : 0.10 % Allowed : 9.56 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.21), residues: 1073 helix: -1.58 (0.15), residues: 826 sheet: None (None), residues: 0 loop : -3.48 (0.31), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 541 HIS 0.005 0.002 HIS B 122 PHE 0.019 0.002 PHE A 59 TYR 0.028 0.002 TYR B 18 ARG 0.004 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8540 (t60) cc_final: 0.7984 (t60) REVERT: C 80 HIS cc_start: 0.8596 (m90) cc_final: 0.7780 (m90) REVERT: C 108 MET cc_start: 0.8411 (mmp) cc_final: 0.8193 (mmm) REVERT: C 171 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7750 (mm-30) REVERT: C 176 PHE cc_start: 0.8060 (p90) cc_final: 0.7729 (p90) REVERT: C 177 MET cc_start: 0.8564 (tmm) cc_final: 0.8223 (tmm) REVERT: C 184 TYR cc_start: 0.8408 (t80) cc_final: 0.8118 (t80) REVERT: B 5 ASN cc_start: 0.7504 (p0) cc_final: 0.6466 (t0) REVERT: B 9 GLN cc_start: 0.8546 (mt0) cc_final: 0.8254 (mt0) REVERT: B 61 LEU cc_start: 0.9519 (mt) cc_final: 0.9126 (tt) REVERT: B 88 PHE cc_start: 0.8664 (m-80) cc_final: 0.8404 (m-80) REVERT: B 92 ASN cc_start: 0.8623 (m-40) cc_final: 0.7918 (m-40) REVERT: B 95 PHE cc_start: 0.8335 (t80) cc_final: 0.7989 (t80) REVERT: B 106 PHE cc_start: 0.8303 (m-80) cc_final: 0.7603 (p90) REVERT: B 114 LEU cc_start: 0.9257 (tp) cc_final: 0.8857 (tp) REVERT: B 119 LYS cc_start: 0.9493 (mtmt) cc_final: 0.8877 (mtmm) REVERT: B 121 PHE cc_start: 0.8439 (m-80) cc_final: 0.8168 (m-80) REVERT: B 163 GLN cc_start: 0.8676 (tt0) cc_final: 0.7983 (tp-100) REVERT: B 186 TYR cc_start: 0.8752 (m-10) cc_final: 0.8539 (m-80) REVERT: B 193 PHE cc_start: 0.8487 (m-80) cc_final: 0.8237 (m-80) REVERT: B 195 MET cc_start: 0.8267 (mtp) cc_final: 0.7949 (ttt) REVERT: B 271 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8676 (mt-10) REVERT: B 289 MET cc_start: 0.7058 (ttm) cc_final: 0.6817 (ttm) REVERT: B 319 LYS cc_start: 0.8967 (mttm) cc_final: 0.8678 (mttm) REVERT: A 49 MET cc_start: 0.7862 (mmm) cc_final: 0.6974 (ppp) REVERT: A 119 ASN cc_start: 0.8981 (m-40) cc_final: 0.8460 (t0) REVERT: A 219 GLU cc_start: 0.8970 (tp30) cc_final: 0.8663 (mm-30) REVERT: A 327 LEU cc_start: 0.9184 (tp) cc_final: 0.8980 (tt) REVERT: A 520 MET cc_start: 0.8618 (mmm) cc_final: 0.8288 (mmm) REVERT: A 577 ASP cc_start: 0.9119 (p0) cc_final: 0.8881 (t70) outliers start: 1 outliers final: 1 residues processed: 316 average time/residue: 0.2289 time to fit residues: 97.6500 Evaluate side-chains 228 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN B 202 ASN B 206 GLN B 210 ASN A 86 GLN A 101 ASN A 117 GLN A 135 ASN A 202 ASN A 336 GLN A 429 ASN A 593 GLN A 661 HIS ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.113460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.084800 restraints weight = 28123.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.087003 restraints weight = 17292.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088484 restraints weight = 12417.203| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9221 Z= 0.185 Angle : 0.641 11.626 12491 Z= 0.339 Chirality : 0.040 0.138 1388 Planarity : 0.005 0.062 1546 Dihedral : 5.037 27.065 1204 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.51 % Allowed : 4.37 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1073 helix: 0.53 (0.17), residues: 828 sheet: None (None), residues: 0 loop : -2.74 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 123 HIS 0.007 0.001 HIS C 123 PHE 0.050 0.002 PHE B 152 TYR 0.021 0.001 TYR C 44 ARG 0.006 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 303 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8173 (t60) cc_final: 0.7861 (t60) REVERT: C 44 TYR cc_start: 0.7300 (t80) cc_final: 0.6838 (t80) REVERT: C 45 ASP cc_start: 0.8038 (p0) cc_final: 0.7451 (p0) REVERT: C 80 HIS cc_start: 0.8783 (m90) cc_final: 0.8197 (m90) REVERT: C 81 LEU cc_start: 0.9403 (mt) cc_final: 0.8894 (mt) REVERT: C 85 GLU cc_start: 0.8684 (tp30) cc_final: 0.7932 (pt0) REVERT: C 96 TRP cc_start: 0.4819 (m-10) cc_final: 0.4390 (m-10) REVERT: C 99 PHE cc_start: 0.8676 (m-80) cc_final: 0.8414 (m-10) REVERT: C 171 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6449 (mt-10) REVERT: C 176 PHE cc_start: 0.7928 (p90) cc_final: 0.7595 (p90) REVERT: C 177 MET cc_start: 0.8725 (tmm) cc_final: 0.8453 (tmm) REVERT: C 184 TYR cc_start: 0.8725 (t80) cc_final: 0.8354 (t80) REVERT: B 5 ASN cc_start: 0.6970 (p0) cc_final: 0.6493 (t0) REVERT: B 37 GLN cc_start: 0.9198 (tt0) cc_final: 0.8754 (tm-30) REVERT: B 61 LEU cc_start: 0.9407 (mt) cc_final: 0.9167 (tt) REVERT: B 64 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8950 (tm-30) REVERT: B 88 PHE cc_start: 0.8750 (m-80) cc_final: 0.8467 (t80) REVERT: B 95 PHE cc_start: 0.8716 (t80) cc_final: 0.8473 (t80) REVERT: B 106 PHE cc_start: 0.8162 (m-80) cc_final: 0.7455 (p90) REVERT: B 114 LEU cc_start: 0.9427 (tp) cc_final: 0.8876 (tp) REVERT: B 118 LEU cc_start: 0.9475 (mm) cc_final: 0.9116 (mm) REVERT: B 119 LYS cc_start: 0.9625 (mtmt) cc_final: 0.9239 (mtmm) REVERT: B 121 PHE cc_start: 0.8787 (m-80) cc_final: 0.8231 (m-80) REVERT: B 152 PHE cc_start: 0.7689 (m-80) cc_final: 0.7362 (m-80) REVERT: B 163 GLN cc_start: 0.8762 (tt0) cc_final: 0.7992 (tp-100) REVERT: B 175 ASN cc_start: 0.8329 (m-40) cc_final: 0.7683 (p0) REVERT: B 186 TYR cc_start: 0.8961 (m-10) cc_final: 0.8698 (m-80) REVERT: B 191 MET cc_start: 0.9111 (tmm) cc_final: 0.8813 (tmm) REVERT: B 193 PHE cc_start: 0.8944 (m-80) cc_final: 0.8675 (m-80) REVERT: B 274 ILE cc_start: 0.9361 (mt) cc_final: 0.9087 (tt) REVERT: B 286 HIS cc_start: 0.8137 (m-70) cc_final: 0.7744 (m-70) REVERT: B 289 MET cc_start: 0.7195 (ttm) cc_final: 0.6830 (ttm) REVERT: A 49 MET cc_start: 0.7871 (mmm) cc_final: 0.6958 (ppp) REVERT: A 119 ASN cc_start: 0.8946 (m-40) cc_final: 0.8546 (t0) REVERT: A 219 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8632 (mm-30) REVERT: A 238 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7857 (mt-10) REVERT: A 327 LEU cc_start: 0.9226 (tp) cc_final: 0.8958 (tt) REVERT: A 388 LYS cc_start: 0.9019 (mmmm) cc_final: 0.8582 (mmtm) REVERT: A 402 LEU cc_start: 0.9406 (tt) cc_final: 0.9093 (tt) REVERT: A 438 MET cc_start: 0.9090 (mmp) cc_final: 0.8579 (mmm) REVERT: A 472 LEU cc_start: 0.9434 (mt) cc_final: 0.8943 (mt) REVERT: A 473 MET cc_start: 0.8064 (mmm) cc_final: 0.7708 (mmm) REVERT: A 474 GLU cc_start: 0.9267 (pt0) cc_final: 0.9042 (pt0) REVERT: A 479 ASN cc_start: 0.8678 (m-40) cc_final: 0.8477 (m-40) REVERT: A 481 PHE cc_start: 0.8058 (t80) cc_final: 0.7494 (t80) REVERT: A 520 MET cc_start: 0.8600 (mmm) cc_final: 0.8236 (mmm) REVERT: A 577 ASP cc_start: 0.9196 (p0) cc_final: 0.8592 (t70) REVERT: A 675 LYS cc_start: 0.8282 (tttt) cc_final: 0.7695 (tptm) outliers start: 5 outliers final: 1 residues processed: 305 average time/residue: 0.1954 time to fit residues: 83.2518 Evaluate side-chains 237 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 8 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 GLN C 175 ASN C 180 HIS ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 564 GLN A 663 HIS ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.109042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.080952 restraints weight = 29333.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.083097 restraints weight = 18075.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.084505 restraints weight = 12949.810| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9221 Z= 0.313 Angle : 0.696 10.112 12491 Z= 0.373 Chirality : 0.043 0.145 1388 Planarity : 0.005 0.063 1546 Dihedral : 5.161 26.791 1204 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.24), residues: 1073 helix: 0.76 (0.17), residues: 836 sheet: None (None), residues: 0 loop : -2.74 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 68 HIS 0.005 0.001 HIS A 661 PHE 0.027 0.002 PHE B 152 TYR 0.022 0.002 TYR C 44 ARG 0.011 0.001 ARG B 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8077 (t60) cc_final: 0.7724 (t60) REVERT: C 45 ASP cc_start: 0.7958 (p0) cc_final: 0.7616 (p0) REVERT: C 80 HIS cc_start: 0.8602 (m90) cc_final: 0.8062 (m90) REVERT: C 81 LEU cc_start: 0.9427 (mt) cc_final: 0.9014 (mt) REVERT: C 85 GLU cc_start: 0.8800 (tp30) cc_final: 0.7961 (pt0) REVERT: C 96 TRP cc_start: 0.5143 (m-10) cc_final: 0.4650 (m-10) REVERT: C 99 PHE cc_start: 0.8578 (m-80) cc_final: 0.8251 (m-10) REVERT: C 176 PHE cc_start: 0.7918 (p90) cc_final: 0.7567 (p90) REVERT: C 177 MET cc_start: 0.8740 (tmm) cc_final: 0.8507 (tmm) REVERT: C 184 TYR cc_start: 0.8792 (t80) cc_final: 0.8506 (t80) REVERT: B 5 ASN cc_start: 0.7003 (p0) cc_final: 0.6716 (t0) REVERT: B 64 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8987 (tm-30) REVERT: B 79 HIS cc_start: 0.8482 (m90) cc_final: 0.8156 (m90) REVERT: B 88 PHE cc_start: 0.8904 (m-80) cc_final: 0.8496 (t80) REVERT: B 106 PHE cc_start: 0.8337 (m-80) cc_final: 0.7394 (p90) REVERT: B 114 LEU cc_start: 0.9429 (tp) cc_final: 0.8878 (tp) REVERT: B 115 LEU cc_start: 0.9576 (tp) cc_final: 0.9313 (tp) REVERT: B 116 LEU cc_start: 0.9496 (tt) cc_final: 0.9269 (tt) REVERT: B 118 LEU cc_start: 0.9558 (mm) cc_final: 0.9251 (mm) REVERT: B 119 LYS cc_start: 0.9697 (mtmt) cc_final: 0.9073 (mtmm) REVERT: B 121 PHE cc_start: 0.8767 (m-80) cc_final: 0.8302 (m-80) REVERT: B 122 HIS cc_start: 0.8691 (m90) cc_final: 0.8363 (m90) REVERT: B 152 PHE cc_start: 0.7801 (m-80) cc_final: 0.7505 (m-80) REVERT: B 163 GLN cc_start: 0.8791 (tt0) cc_final: 0.8010 (tp-100) REVERT: B 186 TYR cc_start: 0.9036 (m-10) cc_final: 0.8835 (m-80) REVERT: B 191 MET cc_start: 0.9108 (tmm) cc_final: 0.8745 (tmm) REVERT: B 193 PHE cc_start: 0.8979 (m-80) cc_final: 0.8670 (m-80) REVERT: B 274 ILE cc_start: 0.9407 (mt) cc_final: 0.8917 (tt) REVERT: B 289 MET cc_start: 0.7244 (ttm) cc_final: 0.6971 (ttm) REVERT: B 306 ASP cc_start: 0.8089 (m-30) cc_final: 0.7876 (m-30) REVERT: B 319 LYS cc_start: 0.8593 (mmpt) cc_final: 0.8326 (mmmt) REVERT: A 119 ASN cc_start: 0.8986 (m-40) cc_final: 0.8595 (t0) REVERT: A 327 LEU cc_start: 0.9332 (tp) cc_final: 0.8942 (pp) REVERT: A 374 GLN cc_start: 0.9277 (mt0) cc_final: 0.8624 (mm-40) REVERT: A 388 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8617 (mmtm) REVERT: A 402 LEU cc_start: 0.9370 (tt) cc_final: 0.9064 (tt) REVERT: A 406 ARG cc_start: 0.8907 (mmt90) cc_final: 0.8692 (mmm-85) REVERT: A 438 MET cc_start: 0.9059 (mmp) cc_final: 0.8716 (mmm) REVERT: A 472 LEU cc_start: 0.9423 (mt) cc_final: 0.8945 (mt) REVERT: A 473 MET cc_start: 0.8296 (mmm) cc_final: 0.7895 (mmm) REVERT: A 481 PHE cc_start: 0.8338 (t80) cc_final: 0.7815 (t80) REVERT: A 577 ASP cc_start: 0.9232 (p0) cc_final: 0.8648 (t70) REVERT: A 642 LEU cc_start: 0.7597 (pp) cc_final: 0.6080 (pp) REVERT: D 775 PHE cc_start: 0.8323 (t80) cc_final: 0.8109 (t80) REVERT: D 785 GLU cc_start: 0.9330 (mp0) cc_final: 0.9104 (mp0) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1914 time to fit residues: 75.6579 Evaluate side-chains 236 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 39 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 ASN A 135 ASN A 336 GLN ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 761 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.112255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.084136 restraints weight = 28486.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.086397 restraints weight = 16942.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.087944 restraints weight = 11862.492| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9221 Z= 0.206 Angle : 0.618 10.697 12491 Z= 0.329 Chirality : 0.041 0.135 1388 Planarity : 0.004 0.061 1546 Dihedral : 4.875 24.716 1204 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.20 % Allowed : 3.36 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1073 helix: 1.24 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -2.50 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 541 HIS 0.004 0.001 HIS B 122 PHE 0.025 0.001 PHE B 152 TYR 0.013 0.001 TYR A 655 ARG 0.005 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 287 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8143 (t60) cc_final: 0.7706 (t60) REVERT: C 45 ASP cc_start: 0.7884 (p0) cc_final: 0.7522 (p0) REVERT: C 80 HIS cc_start: 0.8653 (m90) cc_final: 0.8071 (m90) REVERT: C 81 LEU cc_start: 0.9334 (mt) cc_final: 0.8932 (mt) REVERT: C 85 GLU cc_start: 0.8801 (tp30) cc_final: 0.7740 (pt0) REVERT: C 91 ARG cc_start: 0.6319 (mtt90) cc_final: 0.3940 (ptm160) REVERT: C 96 TRP cc_start: 0.5121 (m-10) cc_final: 0.4506 (m-10) REVERT: C 99 PHE cc_start: 0.8562 (m-80) cc_final: 0.8226 (m-10) REVERT: C 108 MET cc_start: 0.8409 (mmp) cc_final: 0.8164 (mmp) REVERT: C 161 MET cc_start: 0.1757 (mmt) cc_final: 0.1552 (mmt) REVERT: C 176 PHE cc_start: 0.7921 (p90) cc_final: 0.7416 (p90) REVERT: C 177 MET cc_start: 0.8785 (tmm) cc_final: 0.8479 (tmm) REVERT: C 184 TYR cc_start: 0.8757 (t80) cc_final: 0.8425 (t80) REVERT: B 5 ASN cc_start: 0.6886 (p0) cc_final: 0.6556 (t0) REVERT: B 63 TRP cc_start: 0.8185 (t60) cc_final: 0.7898 (t60) REVERT: B 88 PHE cc_start: 0.8862 (m-80) cc_final: 0.8318 (t80) REVERT: B 106 PHE cc_start: 0.8267 (m-80) cc_final: 0.7425 (p90) REVERT: B 114 LEU cc_start: 0.9375 (tp) cc_final: 0.8939 (tp) REVERT: B 117 TYR cc_start: 0.8642 (m-10) cc_final: 0.7959 (m-80) REVERT: B 118 LEU cc_start: 0.9474 (mm) cc_final: 0.9250 (mm) REVERT: B 119 LYS cc_start: 0.9649 (mtmt) cc_final: 0.9261 (mtmm) REVERT: B 121 PHE cc_start: 0.8623 (m-80) cc_final: 0.8207 (m-80) REVERT: B 152 PHE cc_start: 0.7567 (m-80) cc_final: 0.7174 (m-80) REVERT: B 163 GLN cc_start: 0.8707 (tt0) cc_final: 0.7956 (tp-100) REVERT: B 175 ASN cc_start: 0.8403 (m-40) cc_final: 0.7763 (p0) REVERT: B 191 MET cc_start: 0.9067 (tmm) cc_final: 0.8694 (tmm) REVERT: B 193 PHE cc_start: 0.8907 (m-80) cc_final: 0.8642 (m-80) REVERT: B 289 MET cc_start: 0.7123 (ttm) cc_final: 0.6862 (ttm) REVERT: B 319 LYS cc_start: 0.8600 (mmpt) cc_final: 0.8303 (mmmt) REVERT: A 108 THR cc_start: 0.9216 (t) cc_final: 0.8959 (t) REVERT: A 119 ASN cc_start: 0.8819 (m-40) cc_final: 0.8535 (t0) REVERT: A 176 LEU cc_start: 0.9105 (mm) cc_final: 0.8872 (pp) REVERT: A 219 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8565 (mm-30) REVERT: A 327 LEU cc_start: 0.9272 (tp) cc_final: 0.8832 (pp) REVERT: A 388 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8636 (mmtm) REVERT: A 402 LEU cc_start: 0.9344 (tt) cc_final: 0.9060 (tt) REVERT: A 406 ARG cc_start: 0.8749 (mmt90) cc_final: 0.8504 (mmm-85) REVERT: A 438 MET cc_start: 0.9015 (mmp) cc_final: 0.8774 (mmm) REVERT: A 472 LEU cc_start: 0.9327 (mt) cc_final: 0.8925 (mm) REVERT: A 473 MET cc_start: 0.8122 (mmm) cc_final: 0.7750 (mmm) REVERT: A 481 PHE cc_start: 0.8125 (t80) cc_final: 0.7506 (t80) REVERT: A 520 MET cc_start: 0.8098 (mmm) cc_final: 0.7788 (mmm) REVERT: A 552 GLU cc_start: 0.8940 (pp20) cc_final: 0.8356 (pp20) REVERT: A 577 ASP cc_start: 0.9191 (p0) cc_final: 0.8651 (t70) REVERT: A 675 LYS cc_start: 0.8420 (tttt) cc_final: 0.7771 (tptm) outliers start: 2 outliers final: 0 residues processed: 287 average time/residue: 0.2094 time to fit residues: 86.7409 Evaluate side-chains 235 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 ASN A 135 ASN A 336 GLN ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.114233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.086361 restraints weight = 28285.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088588 restraints weight = 17374.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090096 restraints weight = 12401.404| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9221 Z= 0.157 Angle : 0.601 9.853 12491 Z= 0.314 Chirality : 0.039 0.147 1388 Planarity : 0.004 0.060 1546 Dihedral : 4.625 21.945 1204 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1073 helix: 1.65 (0.17), residues: 831 sheet: None (None), residues: 0 loop : -2.47 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 541 HIS 0.005 0.001 HIS C 180 PHE 0.021 0.001 PHE C 61 TYR 0.034 0.001 TYR C 44 ARG 0.006 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8150 (t60) cc_final: 0.7826 (t60) REVERT: C 45 ASP cc_start: 0.7998 (p0) cc_final: 0.7253 (p0) REVERT: C 80 HIS cc_start: 0.8641 (m90) cc_final: 0.8247 (m90) REVERT: C 81 LEU cc_start: 0.9312 (mt) cc_final: 0.8471 (pp) REVERT: C 85 GLU cc_start: 0.8933 (tp30) cc_final: 0.7848 (pt0) REVERT: C 91 ARG cc_start: 0.6042 (mtt90) cc_final: 0.3937 (ptm160) REVERT: C 96 TRP cc_start: 0.5161 (m-10) cc_final: 0.4554 (m-10) REVERT: C 99 PHE cc_start: 0.8583 (m-80) cc_final: 0.8268 (m-10) REVERT: C 104 ILE cc_start: 0.8699 (tp) cc_final: 0.8403 (pt) REVERT: C 176 PHE cc_start: 0.8123 (p90) cc_final: 0.7630 (p90) REVERT: C 177 MET cc_start: 0.8801 (tmm) cc_final: 0.8469 (tmm) REVERT: C 184 TYR cc_start: 0.8733 (t80) cc_final: 0.8418 (t80) REVERT: B 5 ASN cc_start: 0.6905 (p0) cc_final: 0.6308 (t0) REVERT: B 79 HIS cc_start: 0.8324 (m90) cc_final: 0.8004 (m90) REVERT: B 85 ARG cc_start: 0.9133 (mpt-90) cc_final: 0.8887 (mtt90) REVERT: B 88 PHE cc_start: 0.8891 (m-80) cc_final: 0.8375 (t80) REVERT: B 106 PHE cc_start: 0.8283 (m-80) cc_final: 0.7494 (p90) REVERT: B 114 LEU cc_start: 0.9398 (tp) cc_final: 0.8829 (tp) REVERT: B 118 LEU cc_start: 0.9520 (mm) cc_final: 0.9266 (mm) REVERT: B 119 LYS cc_start: 0.9548 (mtmt) cc_final: 0.9188 (mtmm) REVERT: B 121 PHE cc_start: 0.8702 (m-80) cc_final: 0.8267 (m-80) REVERT: B 152 PHE cc_start: 0.7266 (m-80) cc_final: 0.6905 (m-80) REVERT: B 163 GLN cc_start: 0.8691 (tt0) cc_final: 0.7940 (tp-100) REVERT: B 164 ILE cc_start: 0.9177 (mt) cc_final: 0.8881 (mm) REVERT: B 175 ASN cc_start: 0.8513 (m-40) cc_final: 0.7928 (p0) REVERT: B 191 MET cc_start: 0.9039 (tmm) cc_final: 0.8613 (tmm) REVERT: B 193 PHE cc_start: 0.9036 (m-80) cc_final: 0.8664 (m-80) REVERT: B 319 LYS cc_start: 0.8624 (mmpt) cc_final: 0.8308 (mmmt) REVERT: A 119 ASN cc_start: 0.8920 (m-40) cc_final: 0.8532 (t0) REVERT: A 152 MET cc_start: 0.8689 (tpt) cc_final: 0.8141 (tpt) REVERT: A 176 LEU cc_start: 0.9092 (mm) cc_final: 0.8861 (pp) REVERT: A 219 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8503 (mm-30) REVERT: A 327 LEU cc_start: 0.9228 (tp) cc_final: 0.8774 (pp) REVERT: A 329 ASP cc_start: 0.8207 (t0) cc_final: 0.7996 (t0) REVERT: A 336 GLN cc_start: 0.8980 (tt0) cc_final: 0.8636 (tt0) REVERT: A 388 LYS cc_start: 0.8875 (mmmm) cc_final: 0.8500 (mmtm) REVERT: A 402 LEU cc_start: 0.9383 (tt) cc_final: 0.8985 (tt) REVERT: A 406 ARG cc_start: 0.8793 (mmt90) cc_final: 0.8481 (mmm-85) REVERT: A 438 MET cc_start: 0.8882 (mmp) cc_final: 0.8657 (mmm) REVERT: A 472 LEU cc_start: 0.9339 (mt) cc_final: 0.8958 (mm) REVERT: A 473 MET cc_start: 0.8318 (mmm) cc_final: 0.7905 (mmm) REVERT: A 481 PHE cc_start: 0.8015 (t80) cc_final: 0.7212 (t80) REVERT: A 520 MET cc_start: 0.8204 (mmm) cc_final: 0.7899 (mmm) REVERT: A 552 GLU cc_start: 0.8925 (pp20) cc_final: 0.8508 (pp20) REVERT: A 577 ASP cc_start: 0.9251 (p0) cc_final: 0.8669 (t70) REVERT: A 619 TYR cc_start: 0.9212 (m-80) cc_final: 0.8938 (m-80) REVERT: A 675 LYS cc_start: 0.8356 (tttt) cc_final: 0.7778 (tptm) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.1899 time to fit residues: 78.4704 Evaluate side-chains 240 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 210 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN A 633 ASN ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.110595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.082176 restraints weight = 28813.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.084401 restraints weight = 17331.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.085806 restraints weight = 12278.073| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9221 Z= 0.300 Angle : 0.691 9.581 12491 Z= 0.369 Chirality : 0.043 0.153 1388 Planarity : 0.004 0.061 1546 Dihedral : 4.927 24.820 1204 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1073 helix: 1.22 (0.17), residues: 832 sheet: None (None), residues: 0 loop : -2.46 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 541 HIS 0.005 0.002 HIS B 81 PHE 0.020 0.002 PHE A 59 TYR 0.040 0.002 TYR C 44 ARG 0.005 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 1.196 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: C 19 TRP cc_start: 0.8049 (t60) cc_final: 0.7763 (t60) REVERT: C 45 ASP cc_start: 0.7905 (p0) cc_final: 0.7375 (p0) REVERT: C 80 HIS cc_start: 0.8738 (m90) cc_final: 0.8262 (m90) REVERT: C 85 GLU cc_start: 0.8900 (tp30) cc_final: 0.8677 (tp30) REVERT: C 91 ARG cc_start: 0.6059 (mtt90) cc_final: 0.3762 (ptm160) REVERT: C 96 TRP cc_start: 0.5320 (m-10) cc_final: 0.4662 (m-10) REVERT: C 99 PHE cc_start: 0.8489 (m-80) cc_final: 0.8205 (m-10) REVERT: C 104 ILE cc_start: 0.8719 (tp) cc_final: 0.8413 (pt) REVERT: C 176 PHE cc_start: 0.8185 (p90) cc_final: 0.7765 (p90) REVERT: C 177 MET cc_start: 0.8769 (tmm) cc_final: 0.8415 (tmm) REVERT: C 184 TYR cc_start: 0.8839 (t80) cc_final: 0.8470 (t80) REVERT: B 5 ASN cc_start: 0.7011 (p0) cc_final: 0.6174 (t0) REVERT: B 88 PHE cc_start: 0.8863 (m-80) cc_final: 0.8315 (t80) REVERT: B 106 PHE cc_start: 0.8342 (m-80) cc_final: 0.7484 (p90) REVERT: B 114 LEU cc_start: 0.9413 (tp) cc_final: 0.8808 (tp) REVERT: B 118 LEU cc_start: 0.9548 (mm) cc_final: 0.9325 (mm) REVERT: B 119 LYS cc_start: 0.9586 (mtmt) cc_final: 0.9169 (mtmm) REVERT: B 121 PHE cc_start: 0.8800 (m-80) cc_final: 0.8315 (m-80) REVERT: B 122 HIS cc_start: 0.8714 (m90) cc_final: 0.8429 (m90) REVERT: B 163 GLN cc_start: 0.8580 (tt0) cc_final: 0.8040 (tp-100) REVERT: B 175 ASN cc_start: 0.8684 (m-40) cc_final: 0.8092 (p0) REVERT: B 191 MET cc_start: 0.9054 (tmm) cc_final: 0.8696 (tmm) REVERT: B 193 PHE cc_start: 0.9008 (m-80) cc_final: 0.8650 (m-80) REVERT: A 119 ASN cc_start: 0.9021 (m-40) cc_final: 0.8684 (t0) REVERT: A 176 LEU cc_start: 0.9125 (mm) cc_final: 0.8911 (pp) REVERT: A 219 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8526 (mm-30) REVERT: A 327 LEU cc_start: 0.9298 (tp) cc_final: 0.9049 (tt) REVERT: A 388 LYS cc_start: 0.9002 (mmmm) cc_final: 0.8670 (mmtm) REVERT: A 402 LEU cc_start: 0.9466 (tt) cc_final: 0.9053 (tt) REVERT: A 406 ARG cc_start: 0.8814 (mmt90) cc_final: 0.8466 (mmm-85) REVERT: A 437 TYR cc_start: 0.9065 (m-10) cc_final: 0.8765 (m-80) REVERT: A 438 MET cc_start: 0.8989 (mmp) cc_final: 0.8758 (mmm) REVERT: A 472 LEU cc_start: 0.9367 (mt) cc_final: 0.9126 (mm) REVERT: A 473 MET cc_start: 0.8445 (mmm) cc_final: 0.8016 (mmm) REVERT: A 481 PHE cc_start: 0.8415 (t80) cc_final: 0.7795 (t80) REVERT: A 520 MET cc_start: 0.8442 (mmm) cc_final: 0.7984 (mmm) REVERT: A 577 ASP cc_start: 0.9226 (p0) cc_final: 0.8793 (t70) REVERT: A 675 LYS cc_start: 0.8370 (tttt) cc_final: 0.7656 (tptm) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.1830 time to fit residues: 71.5933 Evaluate side-chains 226 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 0.0570 chunk 104 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 74 optimal weight: 0.0170 chunk 5 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 105 optimal weight: 30.0000 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN B 210 ASN A 336 GLN A 595 ASN A 633 ASN ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.114099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.085552 restraints weight = 28598.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087845 restraints weight = 17297.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.089384 restraints weight = 12241.883| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9221 Z= 0.169 Angle : 0.626 11.006 12491 Z= 0.327 Chirality : 0.040 0.177 1388 Planarity : 0.004 0.062 1546 Dihedral : 4.689 22.539 1204 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1073 helix: 1.51 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -2.33 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 541 HIS 0.005 0.001 HIS C 180 PHE 0.013 0.001 PHE C 176 TYR 0.050 0.001 TYR C 44 ARG 0.007 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8098 (t60) cc_final: 0.7795 (t60) REVERT: C 45 ASP cc_start: 0.7943 (p0) cc_final: 0.7526 (p0) REVERT: C 80 HIS cc_start: 0.8722 (m90) cc_final: 0.8287 (m-70) REVERT: C 81 LEU cc_start: 0.9293 (mt) cc_final: 0.8441 (pp) REVERT: C 85 GLU cc_start: 0.8849 (tp30) cc_final: 0.7845 (pt0) REVERT: C 91 ARG cc_start: 0.5948 (mtt90) cc_final: 0.3709 (ptm160) REVERT: C 99 PHE cc_start: 0.8474 (m-80) cc_final: 0.8184 (m-10) REVERT: C 104 ILE cc_start: 0.8713 (tp) cc_final: 0.8420 (pt) REVERT: C 176 PHE cc_start: 0.8160 (p90) cc_final: 0.7692 (p90) REVERT: C 177 MET cc_start: 0.8792 (tmm) cc_final: 0.8432 (tmm) REVERT: B 5 ASN cc_start: 0.7038 (p0) cc_final: 0.6191 (t0) REVERT: B 88 PHE cc_start: 0.8887 (m-80) cc_final: 0.8360 (t80) REVERT: B 106 PHE cc_start: 0.8270 (m-80) cc_final: 0.7510 (p90) REVERT: B 114 LEU cc_start: 0.9364 (tp) cc_final: 0.8731 (tp) REVERT: B 115 LEU cc_start: 0.9595 (tp) cc_final: 0.9383 (tp) REVERT: B 119 LYS cc_start: 0.9512 (mtmt) cc_final: 0.9024 (mtmm) REVERT: B 121 PHE cc_start: 0.8698 (m-80) cc_final: 0.8310 (m-80) REVERT: B 152 PHE cc_start: 0.7253 (m-80) cc_final: 0.6696 (m-80) REVERT: B 163 GLN cc_start: 0.8681 (tt0) cc_final: 0.8111 (tp-100) REVERT: B 164 ILE cc_start: 0.9189 (mt) cc_final: 0.8886 (mm) REVERT: B 175 ASN cc_start: 0.8572 (m-40) cc_final: 0.8119 (p0) REVERT: B 191 MET cc_start: 0.9069 (tmm) cc_final: 0.8669 (tmm) REVERT: B 193 PHE cc_start: 0.8990 (m-80) cc_final: 0.8661 (m-80) REVERT: A 119 ASN cc_start: 0.8980 (m-40) cc_final: 0.8610 (t0) REVERT: A 176 LEU cc_start: 0.9095 (mm) cc_final: 0.8887 (pp) REVERT: A 216 ASP cc_start: 0.8560 (t0) cc_final: 0.8232 (t0) REVERT: A 219 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8477 (mm-30) REVERT: A 327 LEU cc_start: 0.9215 (tp) cc_final: 0.8745 (pp) REVERT: A 336 GLN cc_start: 0.8990 (tt0) cc_final: 0.8759 (tt0) REVERT: A 374 GLN cc_start: 0.9064 (mt0) cc_final: 0.8387 (mm-40) REVERT: A 388 LYS cc_start: 0.8823 (mmmm) cc_final: 0.8440 (mmtm) REVERT: A 402 LEU cc_start: 0.9423 (tt) cc_final: 0.8974 (tt) REVERT: A 406 ARG cc_start: 0.8819 (mmt90) cc_final: 0.8451 (mmm-85) REVERT: A 472 LEU cc_start: 0.9303 (mt) cc_final: 0.8915 (mm) REVERT: A 473 MET cc_start: 0.8303 (mmm) cc_final: 0.7910 (mmm) REVERT: A 481 PHE cc_start: 0.8127 (t80) cc_final: 0.7402 (t80) REVERT: A 520 MET cc_start: 0.8240 (mmm) cc_final: 0.7988 (mmm) REVERT: A 552 GLU cc_start: 0.8904 (pp20) cc_final: 0.8553 (pp20) REVERT: A 577 ASP cc_start: 0.9231 (p0) cc_final: 0.8594 (t70) REVERT: A 619 TYR cc_start: 0.9182 (m-80) cc_final: 0.8947 (m-80) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1997 time to fit residues: 80.7989 Evaluate side-chains 233 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 33 optimal weight: 0.0770 chunk 99 optimal weight: 0.0370 chunk 46 optimal weight: 4.9990 overall best weight: 2.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** D 745 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 = 0.3716 r_free = 0.3716 target = 0.112853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.084824 restraints weight = 28780.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.087084 restraints weight = 17192.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.088562 restraints weight = 12126.388| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9221 Z= 0.196 Angle : 0.647 10.580 12491 Z= 0.339 Chirality : 0.041 0.166 1388 Planarity : 0.004 0.061 1546 Dihedral : 4.658 21.540 1204 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.25), residues: 1073 helix: 1.59 (0.17), residues: 833 sheet: None (None), residues: 0 loop : -2.29 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 541 HIS 0.004 0.001 HIS C 180 PHE 0.051 0.001 PHE B 152 TYR 0.048 0.002 TYR C 44 ARG 0.007 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8077 (t60) cc_final: 0.7796 (t60) REVERT: C 45 ASP cc_start: 0.7808 (p0) cc_final: 0.7461 (p0) REVERT: C 80 HIS cc_start: 0.8785 (m90) cc_final: 0.8367 (m90) REVERT: C 81 LEU cc_start: 0.9254 (mt) cc_final: 0.8327 (pp) REVERT: C 85 GLU cc_start: 0.8835 (tp30) cc_final: 0.7812 (pt0) REVERT: C 91 ARG cc_start: 0.5979 (mtt90) cc_final: 0.3774 (ptm160) REVERT: C 99 PHE cc_start: 0.8479 (m-80) cc_final: 0.8181 (m-10) REVERT: C 104 ILE cc_start: 0.8737 (tp) cc_final: 0.8426 (pt) REVERT: C 176 PHE cc_start: 0.8244 (p90) cc_final: 0.7923 (p90) REVERT: C 177 MET cc_start: 0.8832 (tmm) cc_final: 0.8497 (tmm) REVERT: B 5 ASN cc_start: 0.7086 (p0) cc_final: 0.4974 (t0) REVERT: B 9 GLN cc_start: 0.8143 (tt0) cc_final: 0.7571 (mt0) REVERT: B 79 HIS cc_start: 0.8400 (m90) cc_final: 0.8193 (m90) REVERT: B 88 PHE cc_start: 0.8886 (m-80) cc_final: 0.8340 (t80) REVERT: B 106 PHE cc_start: 0.8253 (m-80) cc_final: 0.7467 (p90) REVERT: B 114 LEU cc_start: 0.9420 (tp) cc_final: 0.8973 (tp) REVERT: B 115 LEU cc_start: 0.9620 (tp) cc_final: 0.9403 (tp) REVERT: B 118 LEU cc_start: 0.9518 (mm) cc_final: 0.9278 (mm) REVERT: B 119 LYS cc_start: 0.9540 (mtmt) cc_final: 0.9037 (mtmm) REVERT: B 121 PHE cc_start: 0.8783 (m-80) cc_final: 0.8327 (m-80) REVERT: B 152 PHE cc_start: 0.7211 (m-80) cc_final: 0.6908 (m-80) REVERT: B 163 GLN cc_start: 0.8536 (tt0) cc_final: 0.8003 (tp-100) REVERT: B 164 ILE cc_start: 0.9199 (mt) cc_final: 0.8914 (mm) REVERT: B 175 ASN cc_start: 0.8549 (m-40) cc_final: 0.8076 (p0) REVERT: B 191 MET cc_start: 0.9051 (tmm) cc_final: 0.8680 (tmm) REVERT: B 193 PHE cc_start: 0.9028 (m-80) cc_final: 0.8678 (m-80) REVERT: B 211 PHE cc_start: 0.8243 (t80) cc_final: 0.7829 (t80) REVERT: B 298 MET cc_start: 0.8946 (tmm) cc_final: 0.8666 (tmm) REVERT: B 312 GLN cc_start: 0.7155 (mm-40) cc_final: 0.6895 (mp10) REVERT: A 119 ASN cc_start: 0.9029 (m-40) cc_final: 0.8623 (t0) REVERT: A 219 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8408 (mm-30) REVERT: A 327 LEU cc_start: 0.9219 (tp) cc_final: 0.8747 (pp) REVERT: A 336 GLN cc_start: 0.9012 (tt0) cc_final: 0.8627 (tt0) REVERT: A 374 GLN cc_start: 0.9098 (mt0) cc_final: 0.8448 (mm-40) REVERT: A 388 LYS cc_start: 0.8808 (mmmm) cc_final: 0.8449 (mmtm) REVERT: A 402 LEU cc_start: 0.9423 (tt) cc_final: 0.8963 (tt) REVERT: A 406 ARG cc_start: 0.8868 (mmt90) cc_final: 0.8463 (mmm-85) REVERT: A 472 LEU cc_start: 0.9263 (mt) cc_final: 0.9018 (mm) REVERT: A 473 MET cc_start: 0.8392 (mmm) cc_final: 0.7980 (mmm) REVERT: A 481 PHE cc_start: 0.8211 (t80) cc_final: 0.7512 (t80) REVERT: A 520 MET cc_start: 0.8328 (mmm) cc_final: 0.8044 (mmm) REVERT: A 552 GLU cc_start: 0.8971 (pp20) cc_final: 0.8576 (pp20) REVERT: A 577 ASP cc_start: 0.9200 (p0) cc_final: 0.8594 (t70) REVERT: A 619 TYR cc_start: 0.9122 (m-80) cc_final: 0.8853 (m-80) REVERT: A 637 MET cc_start: 0.7690 (tpt) cc_final: 0.7457 (tpp) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.1769 time to fit residues: 70.6974 Evaluate side-chains 235 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 595 ASN A 633 ASN A 640 HIS ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.110758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.082528 restraints weight = 29011.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.084709 restraints weight = 17597.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.086148 restraints weight = 12530.368| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9221 Z= 0.267 Angle : 0.689 10.189 12491 Z= 0.365 Chirality : 0.043 0.183 1388 Planarity : 0.005 0.060 1546 Dihedral : 4.845 23.923 1204 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.25), residues: 1073 helix: 1.43 (0.17), residues: 833 sheet: None (None), residues: 0 loop : -2.29 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 541 HIS 0.005 0.001 HIS A 640 PHE 0.041 0.002 PHE B 152 TYR 0.023 0.002 TYR A 606 ARG 0.007 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.981 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: C 19 TRP cc_start: 0.8021 (t60) cc_final: 0.7783 (t60) REVERT: C 80 HIS cc_start: 0.8769 (m90) cc_final: 0.8284 (m90) REVERT: C 91 ARG cc_start: 0.6046 (mtt90) cc_final: 0.3863 (ptm160) REVERT: C 99 PHE cc_start: 0.8489 (m-80) cc_final: 0.8191 (m-10) REVERT: C 104 ILE cc_start: 0.8783 (tp) cc_final: 0.8479 (pt) REVERT: C 112 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7441 (tm-30) REVERT: C 176 PHE cc_start: 0.8155 (p90) cc_final: 0.7839 (p90) REVERT: C 177 MET cc_start: 0.8780 (tmm) cc_final: 0.8404 (tmm) REVERT: B 5 ASN cc_start: 0.7118 (p0) cc_final: 0.4970 (t0) REVERT: B 9 GLN cc_start: 0.8129 (tt0) cc_final: 0.7567 (mt0) REVERT: B 80 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8989 (pt0) REVERT: B 88 PHE cc_start: 0.8861 (m-80) cc_final: 0.8331 (t80) REVERT: B 92 ASN cc_start: 0.8882 (m-40) cc_final: 0.8654 (m-40) REVERT: B 96 MET cc_start: 0.8484 (mpp) cc_final: 0.8244 (mpp) REVERT: B 106 PHE cc_start: 0.8470 (m-80) cc_final: 0.7646 (p90) REVERT: B 114 LEU cc_start: 0.9394 (tp) cc_final: 0.8875 (tp) REVERT: B 118 LEU cc_start: 0.9539 (mm) cc_final: 0.9197 (mm) REVERT: B 119 LYS cc_start: 0.9575 (mtmt) cc_final: 0.9085 (mtmm) REVERT: B 121 PHE cc_start: 0.8776 (m-80) cc_final: 0.8370 (m-80) REVERT: B 122 HIS cc_start: 0.8666 (m90) cc_final: 0.8463 (m90) REVERT: B 152 PHE cc_start: 0.7238 (m-80) cc_final: 0.6879 (m-80) REVERT: B 163 GLN cc_start: 0.8587 (tt0) cc_final: 0.8044 (tp-100) REVERT: B 191 MET cc_start: 0.9041 (tmm) cc_final: 0.8662 (tmm) REVERT: B 193 PHE cc_start: 0.9010 (m-80) cc_final: 0.8671 (m-80) REVERT: B 211 PHE cc_start: 0.7986 (t80) cc_final: 0.7672 (t80) REVERT: B 298 MET cc_start: 0.9047 (tmm) cc_final: 0.8828 (mtt) REVERT: B 312 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6992 (mp10) REVERT: A 119 ASN cc_start: 0.9129 (m-40) cc_final: 0.8694 (t0) REVERT: A 219 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8429 (mm-30) REVERT: A 327 LEU cc_start: 0.9274 (tp) cc_final: 0.9021 (tt) REVERT: A 388 LYS cc_start: 0.8873 (mmmm) cc_final: 0.8525 (mmtm) REVERT: A 402 LEU cc_start: 0.9473 (tt) cc_final: 0.8997 (tt) REVERT: A 406 ARG cc_start: 0.8911 (mmt90) cc_final: 0.8502 (mmm-85) REVERT: A 473 MET cc_start: 0.8337 (mmm) cc_final: 0.7954 (mmm) REVERT: A 481 PHE cc_start: 0.8276 (t80) cc_final: 0.7747 (t80) REVERT: A 520 MET cc_start: 0.8335 (mmm) cc_final: 0.8086 (mmm) REVERT: A 577 ASP cc_start: 0.9081 (p0) cc_final: 0.8678 (t70) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1833 time to fit residues: 73.1887 Evaluate side-chains 231 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 98 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 92 optimal weight: 0.1980 chunk 33 optimal weight: 0.0970 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 GLN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 595 ASN A 633 ASN ** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.113743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.085212 restraints weight = 28729.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.087573 restraints weight = 17010.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.089128 restraints weight = 11921.768| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9221 Z= 0.174 Angle : 0.663 10.395 12491 Z= 0.339 Chirality : 0.041 0.192 1388 Planarity : 0.004 0.061 1546 Dihedral : 4.667 21.938 1204 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1073 helix: 1.62 (0.17), residues: 836 sheet: None (None), residues: 0 loop : -2.24 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 541 HIS 0.003 0.001 HIS C 180 PHE 0.040 0.001 PHE B 152 TYR 0.018 0.001 TYR C 44 ARG 0.008 0.000 ARG C 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8004 (t60) cc_final: 0.7747 (t60) REVERT: C 80 HIS cc_start: 0.8772 (m90) cc_final: 0.8381 (m-70) REVERT: C 81 LEU cc_start: 0.9270 (mt) cc_final: 0.8811 (pp) REVERT: C 91 ARG cc_start: 0.5886 (mtt90) cc_final: 0.3944 (ptm160) REVERT: C 99 PHE cc_start: 0.8475 (m-80) cc_final: 0.8168 (m-10) REVERT: C 104 ILE cc_start: 0.8709 (tp) cc_final: 0.8398 (pt) REVERT: C 176 PHE cc_start: 0.8294 (p90) cc_final: 0.7978 (p90) REVERT: C 177 MET cc_start: 0.8773 (tmm) cc_final: 0.8358 (tmm) REVERT: B 5 ASN cc_start: 0.7063 (p0) cc_final: 0.5028 (t0) REVERT: B 9 GLN cc_start: 0.8227 (tt0) cc_final: 0.7669 (mt0) REVERT: B 79 HIS cc_start: 0.8434 (m90) cc_final: 0.8152 (m90) REVERT: B 80 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8970 (pt0) REVERT: B 88 PHE cc_start: 0.8868 (m-80) cc_final: 0.8292 (t80) REVERT: B 92 ASN cc_start: 0.8919 (m-40) cc_final: 0.8717 (m-40) REVERT: B 106 PHE cc_start: 0.8375 (m-80) cc_final: 0.7573 (p90) REVERT: B 114 LEU cc_start: 0.9383 (tp) cc_final: 0.8858 (tp) REVERT: B 115 LEU cc_start: 0.9652 (tp) cc_final: 0.9425 (tp) REVERT: B 117 TYR cc_start: 0.8674 (m-10) cc_final: 0.8068 (m-80) REVERT: B 118 LEU cc_start: 0.9545 (mm) cc_final: 0.9229 (mm) REVERT: B 119 LYS cc_start: 0.9520 (mtmt) cc_final: 0.9038 (mtmm) REVERT: B 121 PHE cc_start: 0.8676 (m-80) cc_final: 0.8329 (m-80) REVERT: B 152 PHE cc_start: 0.7070 (m-80) cc_final: 0.6633 (m-80) REVERT: B 163 GLN cc_start: 0.8549 (tt0) cc_final: 0.8041 (tp-100) REVERT: B 164 ILE cc_start: 0.9189 (mt) cc_final: 0.8898 (mm) REVERT: B 175 ASN cc_start: 0.8989 (m-40) cc_final: 0.8549 (p0) REVERT: B 191 MET cc_start: 0.9086 (tmm) cc_final: 0.8774 (tmm) REVERT: B 193 PHE cc_start: 0.9046 (m-80) cc_final: 0.8685 (m-80) REVERT: B 211 PHE cc_start: 0.7979 (t80) cc_final: 0.7640 (t80) REVERT: B 271 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8728 (mt-10) REVERT: B 312 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6987 (mp10) REVERT: A 119 ASN cc_start: 0.9168 (m-40) cc_final: 0.8724 (t0) REVERT: A 219 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8411 (mm-30) REVERT: A 327 LEU cc_start: 0.9235 (tp) cc_final: 0.8723 (pp) REVERT: A 336 GLN cc_start: 0.9021 (tt0) cc_final: 0.8764 (tt0) REVERT: A 368 TYR cc_start: 0.8993 (m-10) cc_final: 0.8493 (m-10) REVERT: A 374 GLN cc_start: 0.9116 (mt0) cc_final: 0.8473 (mm-40) REVERT: A 388 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8512 (mmtm) REVERT: A 402 LEU cc_start: 0.9450 (tt) cc_final: 0.9042 (tt) REVERT: A 406 ARG cc_start: 0.8943 (mmt90) cc_final: 0.8506 (mmm-85) REVERT: A 472 LEU cc_start: 0.9465 (mm) cc_final: 0.9078 (mm) REVERT: A 473 MET cc_start: 0.8444 (mmm) cc_final: 0.7993 (mmm) REVERT: A 481 PHE cc_start: 0.8156 (t80) cc_final: 0.7538 (t80) REVERT: A 520 MET cc_start: 0.8213 (mmm) cc_final: 0.7976 (mmm) REVERT: A 552 GLU cc_start: 0.8927 (pp20) cc_final: 0.8593 (pp20) REVERT: A 577 ASP cc_start: 0.9235 (p0) cc_final: 0.8606 (t70) REVERT: A 619 TYR cc_start: 0.9155 (m-80) cc_final: 0.8815 (m-80) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1843 time to fit residues: 75.2552 Evaluate side-chains 239 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 59 optimal weight: 0.0770 chunk 67 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 0.0770 chunk 99 optimal weight: 0.2980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 HIS ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** D 745 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 = 0.3757 r_free = 0.3757 target = 0.115860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.087139 restraints weight = 28227.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.089554 restraints weight = 16775.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.091193 restraints weight = 11759.970| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9221 Z= 0.168 Angle : 0.656 10.182 12491 Z= 0.332 Chirality : 0.040 0.193 1388 Planarity : 0.004 0.058 1546 Dihedral : 4.451 19.686 1204 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.26), residues: 1073 helix: 1.80 (0.18), residues: 831 sheet: None (None), residues: 0 loop : -2.11 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 541 HIS 0.003 0.001 HIS A 663 PHE 0.037 0.001 PHE B 152 TYR 0.013 0.001 TYR C 44 ARG 0.008 0.000 ARG C 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3103.61 seconds wall clock time: 55 minutes 5.94 seconds (3305.94 seconds total)