Starting phenix.real_space_refine on Tue Feb 11 09:55:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ehx_28154/02_2025/8ehx_28154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ehx_28154/02_2025/8ehx_28154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ehx_28154/02_2025/8ehx_28154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ehx_28154/02_2025/8ehx_28154.map" model { file = "/net/cci-nas-00/data/ceres_data/8ehx_28154/02_2025/8ehx_28154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ehx_28154/02_2025/8ehx_28154.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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 36 5.16 5 C 3408 2.51 5 N 840 2.21 5 O 869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5153 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5153 Classifications: {'peptide': 631} Link IDs: {'PTRANS': 23, 'TRANS': 607} Chain breaks: 3 Time building chain proxies: 3.50, per 1000 atoms: 0.68 Number of scatterers: 5153 At special positions: 0 Unit cell: (104.775, 83.325, 84.15, 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 36 16.00 O 869 8.00 N 840 7.00 C 3408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 559 " distance=2.03 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: 1.27 Conformation dependent library (CDL) restraints added in 547.7 milliseconds 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1210 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 1 sheets defined 71.9% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 31 through 35 removed outlier: 3.773A pdb=" N GLY A 35 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 39 Processing helix chain 'A' and resid 40 through 67 removed outlier: 3.512A pdb=" N VAL A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N PHE A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 removed outlier: 3.855A pdb=" N PHE A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 172 removed outlier: 3.595A pdb=" N ILE A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N ASP A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 179 Processing helix chain 'A' and resid 189 through 193 removed outlier: 3.726A pdb=" N ARG A 192 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 204 through 228 removed outlier: 3.978A pdb=" N HIS A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.578A pdb=" N ILE A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR A 264 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 306 removed outlier: 3.717A pdb=" N MET A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 Processing helix chain 'A' and resid 368 through 380 removed outlier: 3.987A pdb=" N THR A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 404 through 407 Processing helix chain 'A' and resid 427 through 458 removed outlier: 3.854A pdb=" N TRP A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 478 through 501 Proline residue: A 492 - end of helix removed outlier: 3.967A pdb=" N PHE A 500 " --> pdb=" O TYR A 496 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE A 501 " --> pdb=" O TYR A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 527 Processing helix chain 'A' and resid 527 through 544 removed outlier: 5.095A pdb=" N PHE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 578 removed outlier: 3.614A pdb=" N VAL A 570 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 587 Processing helix chain 'A' and resid 595 through 600 removed outlier: 3.747A pdb=" N LEU A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 612 removed outlier: 4.209A pdb=" N ARG A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN A 609 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 637 removed outlier: 3.758A pdb=" N ALA A 623 " --> pdb=" O GLN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 667 removed outlier: 4.289A pdb=" N PHE A 647 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 651 " --> pdb=" O PHE A 647 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 703 removed outlier: 3.601A pdb=" N SER A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 707 through 726 Processing helix chain 'A' and resid 727 through 729 No H-bonds generated for 'chain 'A' and resid 727 through 729' Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 276 removed outlier: 3.611A pdb=" N GLU A 271 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET A 361 " --> pdb=" O CYS A 275 " (cutoff:3.500A) 307 hydrogen bonds defined for protein. 894 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1169 1.33 - 1.45: 1189 1.45 - 1.57: 2884 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 5296 Sorted by residual: bond pdb=" CG TYR A 616 " pdb=" CD2 TYR A 616 " ideal model delta sigma weight residual 1.389 1.306 0.083 2.10e-02 2.27e+03 1.58e+01 bond pdb=" CE2 TYR A 616 " pdb=" CZ TYR A 616 " ideal model delta sigma weight residual 1.378 1.287 0.091 2.40e-02 1.74e+03 1.45e+01 bond pdb=" N HIS A 422 " pdb=" CA HIS A 422 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.26e-02 6.30e+03 8.36e+00 bond pdb=" CZ ARG A 607 " pdb=" NH1 ARG A 607 " ideal model delta sigma weight residual 1.323 1.284 0.039 1.40e-02 5.10e+03 7.59e+00 bond pdb=" CZ ARG A 29 " pdb=" NH2 ARG A 29 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.38e+00 ... (remaining 5291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 6869 1.84 - 3.68: 258 3.68 - 5.53: 40 5.53 - 7.37: 11 7.37 - 9.21: 2 Bond angle restraints: 7180 Sorted by residual: angle pdb=" N LEU A 591 " pdb=" CA LEU A 591 " pdb=" C LEU A 591 " ideal model delta sigma weight residual 113.97 104.76 9.21 1.28e+00 6.10e-01 5.18e+01 angle pdb=" N ALA A 54 " pdb=" CA ALA A 54 " pdb=" C ALA A 54 " ideal model delta sigma weight residual 113.43 106.62 6.81 1.26e+00 6.30e-01 2.92e+01 angle pdb=" N LEU A 592 " pdb=" CA LEU A 592 " pdb=" C LEU A 592 " ideal model delta sigma weight residual 113.19 107.66 5.53 1.19e+00 7.06e-01 2.16e+01 angle pdb=" N LEU A 53 " pdb=" CA LEU A 53 " pdb=" C LEU A 53 " ideal model delta sigma weight residual 113.21 107.88 5.33 1.15e+00 7.56e-01 2.15e+01 angle pdb=" N PHE A 59 " pdb=" CA PHE A 59 " pdb=" C PHE A 59 " ideal model delta sigma weight residual 111.33 106.52 4.81 1.21e+00 6.83e-01 1.58e+01 ... (remaining 7175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 2644 17.93 - 35.87: 352 35.87 - 53.80: 93 53.80 - 71.73: 12 71.73 - 89.66: 3 Dihedral angle restraints: 3104 sinusoidal: 1235 harmonic: 1869 Sorted by residual: dihedral pdb=" CB CYS A 23 " pdb=" SG CYS A 23 " pdb=" SG CYS A 559 " pdb=" CB CYS A 559 " ideal model delta sinusoidal sigma weight residual -86.00 -157.70 71.70 1 1.00e+01 1.00e-02 6.59e+01 dihedral pdb=" CA LEU A 537 " pdb=" C LEU A 537 " pdb=" N ASP A 538 " pdb=" CA ASP A 538 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA VAL A 278 " pdb=" C VAL A 278 " pdb=" N ALA A 279 " pdb=" CA ALA A 279 " ideal model delta harmonic sigma weight residual 180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 3101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 645 0.055 - 0.110: 139 0.110 - 0.165: 19 0.165 - 0.221: 0 0.221 - 0.276: 5 Chirality restraints: 808 Sorted by residual: chirality pdb=" CA ILE A 61 " pdb=" N ILE A 61 " pdb=" C ILE A 61 " pdb=" CB ILE A 61 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ALA A 604 " pdb=" N ALA A 604 " pdb=" C ALA A 604 " pdb=" CB ALA A 604 " both_signs ideal model delta sigma weight residual False 2.48 2.24 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA LEU A 58 " pdb=" N LEU A 58 " pdb=" C LEU A 58 " pdb=" CB LEU A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 805 not shown) Planarity restraints: 877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 616 " -0.016 2.00e-02 2.50e+03 3.66e-02 2.68e+01 pdb=" CG TYR A 616 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 616 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 616 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 616 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR A 616 " 0.058 2.00e-02 2.50e+03 pdb=" CZ TYR A 616 " -0.035 2.00e-02 2.50e+03 pdb=" OH TYR A 616 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 645 " 0.061 5.00e-02 4.00e+02 9.10e-02 1.33e+01 pdb=" N PRO A 646 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO A 646 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 646 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 229 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" C LYS A 229 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS A 229 " 0.017 2.00e-02 2.50e+03 pdb=" N MET A 230 " 0.015 2.00e-02 2.50e+03 ... (remaining 874 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 804 2.75 - 3.29: 5331 3.29 - 3.83: 8552 3.83 - 4.36: 9629 4.36 - 4.90: 16399 Nonbonded interactions: 40715 Sorted by model distance: nonbonded pdb=" O ASN A 177 " pdb=" ND2 ASN A 197 " model vdw 2.214 3.120 nonbonded pdb=" O MET A 628 " pdb=" OG1 THR A 632 " model vdw 2.215 3.040 nonbonded pdb=" ND2 ASN A 177 " pdb=" O THR A 193 " model vdw 2.263 3.120 nonbonded pdb=" O SER A 603 " pdb=" OG SER A 603 " model vdw 2.267 3.040 nonbonded pdb=" O SER A 60 " pdb=" N ARG A 63 " model vdw 2.299 3.120 ... (remaining 40710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.720 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.820 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.005 0.091 5296 Z= 0.348 Angle : 0.796 9.211 7180 Z= 0.480 Chirality : 0.049 0.276 808 Planarity : 0.006 0.091 877 Dihedral : 17.023 89.662 1891 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.51 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 29.23 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.36), residues: 623 helix: 0.88 (0.27), residues: 402 sheet: 1.80 (1.76), residues: 10 loop : -1.50 (0.48), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 485 HIS 0.007 0.001 HIS A 504 PHE 0.014 0.001 PHE A 59 TYR 0.058 0.002 TYR A 616 ARG 0.016 0.001 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8135 (mt-10) REVERT: A 348 LYS cc_start: 0.8768 (mttt) cc_final: 0.8454 (pttt) REVERT: A 571 ASN cc_start: 0.8675 (m-40) cc_final: 0.8443 (m110) REVERT: A 592 LEU cc_start: 0.7870 (mt) cc_final: 0.7409 (tt) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1784 time to fit residues: 23.4365 Evaluate side-chains 92 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 0.0470 chunk 57 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.183646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.133803 restraints weight = 7513.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138025 restraints weight = 3760.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140118 restraints weight = 2624.595| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5296 Z= 0.201 Angle : 0.580 6.534 7180 Z= 0.308 Chirality : 0.040 0.124 808 Planarity : 0.005 0.070 877 Dihedral : 4.499 26.662 690 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.42 % Favored : 93.26 % Rotamer: Outliers : 4.10 % Allowed : 27.63 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.36), residues: 623 helix: 1.39 (0.26), residues: 409 sheet: 2.22 (1.69), residues: 10 loop : -1.73 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 485 HIS 0.003 0.001 HIS A 150 PHE 0.010 0.001 PHE A 569 TYR 0.032 0.002 TYR A 215 ARG 0.006 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.5907 (mtt) REVERT: A 141 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7830 (tmm-80) REVERT: A 258 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8926 (ttpp) REVERT: A 277 ASN cc_start: 0.6769 (t0) cc_final: 0.6515 (t0) REVERT: A 348 LYS cc_start: 0.8759 (mttt) cc_final: 0.8406 (pttt) REVERT: A 584 ASP cc_start: 0.8500 (t0) cc_final: 0.8095 (t0) REVERT: A 592 LEU cc_start: 0.7708 (mt) cc_final: 0.7169 (tt) REVERT: A 613 HIS cc_start: 0.5311 (t-90) cc_final: 0.4948 (m170) REVERT: A 614 GLN cc_start: 0.7328 (pt0) cc_final: 0.6982 (mm-40) REVERT: A 725 LEU cc_start: 0.8244 (mm) cc_final: 0.8043 (mm) outliers start: 23 outliers final: 13 residues processed: 118 average time/residue: 0.1669 time to fit residues: 26.0352 Evaluate side-chains 109 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 700 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 45 optimal weight: 0.0270 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 581 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.180396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.130500 restraints weight = 7597.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.134587 restraints weight = 3807.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.137090 restraints weight = 2651.225| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5296 Z= 0.200 Angle : 0.549 5.934 7180 Z= 0.290 Chirality : 0.040 0.124 808 Planarity : 0.005 0.062 877 Dihedral : 4.385 26.689 690 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.90 % Favored : 92.78 % Rotamer: Outliers : 6.24 % Allowed : 26.74 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.36), residues: 623 helix: 1.57 (0.26), residues: 416 sheet: 2.66 (1.67), residues: 10 loop : -1.91 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 485 HIS 0.005 0.001 HIS A 150 PHE 0.010 0.001 PHE A 59 TYR 0.036 0.001 TYR A 215 ARG 0.005 0.000 ARG A 556 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6587 (tmm) cc_final: 0.5868 (mtt) REVERT: A 225 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6513 (ttt180) REVERT: A 283 PHE cc_start: 0.7141 (m-80) cc_final: 0.6908 (m-80) REVERT: A 348 LYS cc_start: 0.8751 (mttt) cc_final: 0.8411 (pttt) REVERT: A 592 LEU cc_start: 0.7402 (mt) cc_final: 0.6914 (tt) REVERT: A 613 HIS cc_start: 0.5412 (t-90) cc_final: 0.5170 (m170) REVERT: A 672 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8072 (pt) REVERT: A 730 PHE cc_start: 0.6911 (t80) cc_final: 0.6517 (t80) outliers start: 35 outliers final: 20 residues processed: 123 average time/residue: 0.1653 time to fit residues: 26.9287 Evaluate side-chains 116 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 700 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 38 optimal weight: 0.0770 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.176674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126114 restraints weight = 7803.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130159 restraints weight = 3926.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.132586 restraints weight = 2732.715| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5296 Z= 0.286 Angle : 0.599 6.996 7180 Z= 0.313 Chirality : 0.042 0.160 808 Planarity : 0.005 0.062 877 Dihedral : 4.469 26.783 690 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.90 % Favored : 92.94 % Rotamer: Outliers : 8.02 % Allowed : 24.06 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.36), residues: 623 helix: 1.46 (0.26), residues: 418 sheet: 2.34 (1.57), residues: 10 loop : -1.89 (0.49), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 485 HIS 0.007 0.001 HIS A 259 PHE 0.010 0.001 PHE A 712 TYR 0.034 0.001 TYR A 215 ARG 0.009 0.001 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 98 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6701 (tmm) cc_final: 0.5932 (mtt) REVERT: A 59 PHE cc_start: 0.8995 (t80) cc_final: 0.8715 (t80) REVERT: A 225 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7078 (ttp80) REVERT: A 283 PHE cc_start: 0.7153 (m-80) cc_final: 0.6903 (m-80) REVERT: A 348 LYS cc_start: 0.8813 (mttt) cc_final: 0.8446 (pttt) REVERT: A 477 GLN cc_start: 0.7552 (mt0) cc_final: 0.7221 (mt0) REVERT: A 523 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8053 (tp) REVERT: A 592 LEU cc_start: 0.7320 (mt) cc_final: 0.6789 (tt) REVERT: A 607 ARG cc_start: 0.5091 (ptt-90) cc_final: 0.4558 (ptt-90) REVERT: A 613 HIS cc_start: 0.5570 (t-90) cc_final: 0.5242 (m170) REVERT: A 614 GLN cc_start: 0.7311 (pt0) cc_final: 0.6841 (mm110) REVERT: A 672 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8118 (pt) REVERT: A 730 PHE cc_start: 0.6737 (t80) cc_final: 0.6421 (t80) outliers start: 45 outliers final: 31 residues processed: 130 average time/residue: 0.1559 time to fit residues: 26.7276 Evaluate side-chains 130 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 542 ARG Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 732 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 46 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.178317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128465 restraints weight = 7613.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.132565 restraints weight = 3841.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.135030 restraints weight = 2664.851| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5296 Z= 0.211 Angle : 0.585 9.331 7180 Z= 0.296 Chirality : 0.041 0.249 808 Planarity : 0.005 0.062 877 Dihedral : 4.404 26.847 690 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.10 % Favored : 93.58 % Rotamer: Outliers : 7.13 % Allowed : 25.31 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.36), residues: 623 helix: 1.64 (0.26), residues: 417 sheet: 2.41 (1.58), residues: 10 loop : -1.86 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 485 HIS 0.007 0.001 HIS A 150 PHE 0.010 0.001 PHE A 569 TYR 0.033 0.001 TYR A 215 ARG 0.006 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6706 (tmm) cc_final: 0.5965 (mtt) REVERT: A 59 PHE cc_start: 0.8962 (t80) cc_final: 0.8690 (t80) REVERT: A 67 TRP cc_start: 0.5440 (OUTLIER) cc_final: 0.5204 (m-10) REVERT: A 199 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7180 (mmtt) REVERT: A 206 TRP cc_start: 0.7880 (OUTLIER) cc_final: 0.7585 (m-10) REVERT: A 225 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.7043 (ttp80) REVERT: A 283 PHE cc_start: 0.7083 (m-80) cc_final: 0.6873 (m-80) REVERT: A 348 LYS cc_start: 0.8802 (mttt) cc_final: 0.8451 (pttt) REVERT: A 469 TYR cc_start: 0.8346 (t80) cc_final: 0.8046 (t80) REVERT: A 477 GLN cc_start: 0.7609 (mt0) cc_final: 0.7280 (mt0) REVERT: A 496 TYR cc_start: 0.8009 (m-80) cc_final: 0.7647 (m-80) REVERT: A 523 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7798 (tp) REVERT: A 592 LEU cc_start: 0.7261 (mt) cc_final: 0.6735 (tt) REVERT: A 607 ARG cc_start: 0.5069 (ptt-90) cc_final: 0.4637 (ptt-90) REVERT: A 613 HIS cc_start: 0.5578 (t-90) cc_final: 0.5294 (m170) REVERT: A 614 GLN cc_start: 0.7450 (pt0) cc_final: 0.6721 (mm-40) REVERT: A 619 GLN cc_start: 0.8104 (pt0) cc_final: 0.7347 (pm20) REVERT: A 672 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8075 (pt) REVERT: A 730 PHE cc_start: 0.6814 (t80) cc_final: 0.6546 (t80) outliers start: 40 outliers final: 30 residues processed: 131 average time/residue: 0.1628 time to fit residues: 28.2985 Evaluate side-chains 131 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 67 TRP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 732 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 GLN A 613 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.123819 restraints weight = 7810.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127694 restraints weight = 3985.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.130063 restraints weight = 2784.506| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5296 Z= 0.290 Angle : 0.610 6.718 7180 Z= 0.315 Chirality : 0.042 0.152 808 Planarity : 0.005 0.065 877 Dihedral : 4.484 26.941 690 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.90 % Favored : 92.78 % Rotamer: Outliers : 8.20 % Allowed : 25.49 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.36), residues: 623 helix: 1.60 (0.26), residues: 418 sheet: 2.05 (1.46), residues: 10 loop : -1.78 (0.50), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 485 HIS 0.007 0.001 HIS A 150 PHE 0.013 0.001 PHE A 712 TYR 0.029 0.002 TYR A 215 ARG 0.006 0.000 ARG A 556 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 92 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6752 (tmm) cc_final: 0.6021 (mtt) REVERT: A 59 PHE cc_start: 0.9020 (t80) cc_final: 0.8760 (t80) REVERT: A 67 TRP cc_start: 0.5438 (OUTLIER) cc_final: 0.5206 (m-10) REVERT: A 199 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7302 (mmtt) REVERT: A 206 TRP cc_start: 0.7898 (OUTLIER) cc_final: 0.7574 (m-10) REVERT: A 283 PHE cc_start: 0.7091 (m-80) cc_final: 0.6852 (m-80) REVERT: A 348 LYS cc_start: 0.8826 (mttt) cc_final: 0.8455 (pttt) REVERT: A 469 TYR cc_start: 0.8395 (t80) cc_final: 0.8122 (t80) REVERT: A 523 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8032 (tp) REVERT: A 592 LEU cc_start: 0.7259 (mt) cc_final: 0.6704 (tt) REVERT: A 607 ARG cc_start: 0.5109 (ptt-90) cc_final: 0.4778 (ptt-90) REVERT: A 614 GLN cc_start: 0.7427 (pt0) cc_final: 0.6699 (mm110) REVERT: A 619 GLN cc_start: 0.8132 (pt0) cc_final: 0.7307 (pm20) REVERT: A 672 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8136 (pt) outliers start: 46 outliers final: 33 residues processed: 128 average time/residue: 0.1522 time to fit residues: 25.8023 Evaluate side-chains 128 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 67 TRP Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 732 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 26 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.176663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126801 restraints weight = 7696.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.130772 restraints weight = 3898.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.133303 restraints weight = 2723.087| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5296 Z= 0.209 Angle : 0.617 15.988 7180 Z= 0.304 Chirality : 0.040 0.137 808 Planarity : 0.005 0.065 877 Dihedral : 4.421 26.992 690 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.42 % Favored : 93.42 % Rotamer: Outliers : 7.13 % Allowed : 27.27 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.36), residues: 623 helix: 1.70 (0.26), residues: 419 sheet: 2.16 (1.47), residues: 10 loop : -1.76 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 485 HIS 0.006 0.001 HIS A 150 PHE 0.011 0.001 PHE A 712 TYR 0.029 0.001 TYR A 215 ARG 0.006 0.000 ARG A 556 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6689 (tmm) cc_final: 0.5936 (mtt) REVERT: A 199 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7320 (mmtt) REVERT: A 206 TRP cc_start: 0.7842 (OUTLIER) cc_final: 0.7519 (m-10) REVERT: A 283 PHE cc_start: 0.7084 (m-80) cc_final: 0.6875 (m-80) REVERT: A 348 LYS cc_start: 0.8814 (mttt) cc_final: 0.8444 (pttt) REVERT: A 469 TYR cc_start: 0.8338 (t80) cc_final: 0.8067 (t80) REVERT: A 496 TYR cc_start: 0.8001 (m-80) cc_final: 0.7608 (m-80) REVERT: A 523 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7763 (tp) REVERT: A 592 LEU cc_start: 0.7227 (mt) cc_final: 0.6688 (tt) REVERT: A 619 GLN cc_start: 0.8106 (pt0) cc_final: 0.7380 (pm20) REVERT: A 672 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8175 (pt) outliers start: 40 outliers final: 28 residues processed: 126 average time/residue: 0.1446 time to fit residues: 24.4474 Evaluate side-chains 126 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 558 GLU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 700 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 49 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.175947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125979 restraints weight = 7722.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.129978 restraints weight = 3927.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132385 restraints weight = 2737.016| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5296 Z= 0.233 Angle : 0.625 14.605 7180 Z= 0.309 Chirality : 0.041 0.181 808 Planarity : 0.005 0.068 877 Dihedral : 4.473 27.174 690 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.58 % Favored : 93.26 % Rotamer: Outliers : 6.95 % Allowed : 27.45 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.37), residues: 623 helix: 1.69 (0.26), residues: 419 sheet: 2.08 (1.48), residues: 10 loop : -1.77 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 485 HIS 0.013 0.002 HIS A 732 PHE 0.016 0.001 PHE A 561 TYR 0.030 0.001 TYR A 215 ARG 0.011 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6714 (tmm) cc_final: 0.5954 (mtt) REVERT: A 199 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7340 (mmtt) REVERT: A 206 TRP cc_start: 0.7761 (OUTLIER) cc_final: 0.7389 (m-10) REVERT: A 283 PHE cc_start: 0.7071 (m-80) cc_final: 0.6847 (m-80) REVERT: A 348 LYS cc_start: 0.8827 (mttt) cc_final: 0.8461 (pttt) REVERT: A 469 TYR cc_start: 0.8385 (t80) cc_final: 0.8118 (t80) REVERT: A 496 TYR cc_start: 0.8031 (m-80) cc_final: 0.7639 (m-80) REVERT: A 523 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7989 (tp) REVERT: A 592 LEU cc_start: 0.7181 (mt) cc_final: 0.6546 (tt) REVERT: A 619 GLN cc_start: 0.8117 (pt0) cc_final: 0.7472 (pm20) outliers start: 39 outliers final: 29 residues processed: 123 average time/residue: 0.1469 time to fit residues: 24.0696 Evaluate side-chains 125 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 199 LYS Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 700 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 4 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 732 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.178131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128595 restraints weight = 7716.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132600 restraints weight = 3932.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.135101 restraints weight = 2761.942| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5296 Z= 0.190 Angle : 0.610 14.165 7180 Z= 0.302 Chirality : 0.040 0.142 808 Planarity : 0.005 0.069 877 Dihedral : 4.417 27.049 690 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.90 % Favored : 92.94 % Rotamer: Outliers : 4.63 % Allowed : 29.59 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.37), residues: 623 helix: 1.78 (0.26), residues: 419 sheet: 2.10 (1.50), residues: 10 loop : -1.77 (0.51), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 128 HIS 0.010 0.001 HIS A 732 PHE 0.018 0.001 PHE A 561 TYR 0.031 0.001 TYR A 215 ARG 0.010 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6711 (tmm) cc_final: 0.5965 (mtt) REVERT: A 206 TRP cc_start: 0.7745 (OUTLIER) cc_final: 0.7472 (m-10) REVERT: A 283 PHE cc_start: 0.7036 (m-80) cc_final: 0.6817 (m-80) REVERT: A 348 LYS cc_start: 0.8816 (mttt) cc_final: 0.8447 (pttt) REVERT: A 469 TYR cc_start: 0.8331 (t80) cc_final: 0.8092 (t80) REVERT: A 496 TYR cc_start: 0.7972 (m-80) cc_final: 0.7557 (m-80) REVERT: A 523 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7739 (tp) REVERT: A 614 GLN cc_start: 0.5586 (mm-40) cc_final: 0.5352 (mm110) REVERT: A 619 GLN cc_start: 0.8056 (pt0) cc_final: 0.7430 (pm20) outliers start: 26 outliers final: 23 residues processed: 115 average time/residue: 0.1482 time to fit residues: 22.8066 Evaluate side-chains 119 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 700 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 25 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 0.0570 chunk 38 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.179399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129976 restraints weight = 7675.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.134032 restraints weight = 3910.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136588 restraints weight = 2737.299| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5296 Z= 0.178 Angle : 0.642 14.587 7180 Z= 0.315 Chirality : 0.041 0.234 808 Planarity : 0.005 0.068 877 Dihedral : 4.354 26.964 690 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.90 % Favored : 92.94 % Rotamer: Outliers : 4.28 % Allowed : 30.30 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.37), residues: 623 helix: 1.84 (0.26), residues: 419 sheet: 2.14 (1.51), residues: 10 loop : -1.84 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 128 HIS 0.004 0.001 HIS A 259 PHE 0.019 0.001 PHE A 561 TYR 0.030 0.001 TYR A 215 ARG 0.009 0.000 ARG A 607 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1246 Ramachandran restraints generated. 623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6720 (tmm) cc_final: 0.5924 (mtt) REVERT: A 206 TRP cc_start: 0.7764 (OUTLIER) cc_final: 0.7550 (m-10) REVERT: A 287 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8097 (mt-10) REVERT: A 348 LYS cc_start: 0.8816 (mttt) cc_final: 0.8448 (pttt) REVERT: A 469 TYR cc_start: 0.8334 (t80) cc_final: 0.8050 (t80) REVERT: A 496 TYR cc_start: 0.7922 (m-80) cc_final: 0.7490 (m-80) REVERT: A 523 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7722 (tp) REVERT: A 614 GLN cc_start: 0.5731 (mm-40) cc_final: 0.5392 (mm110) REVERT: A 619 GLN cc_start: 0.8035 (pt0) cc_final: 0.7428 (pm20) outliers start: 24 outliers final: 19 residues processed: 115 average time/residue: 0.1586 time to fit residues: 24.1756 Evaluate side-chains 118 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 700 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.1980 chunk 16 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 36 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.178850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129096 restraints weight = 7720.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133115 restraints weight = 3964.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.135625 restraints weight = 2777.563| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5296 Z= 0.197 Angle : 0.646 13.652 7180 Z= 0.320 Chirality : 0.041 0.212 808 Planarity : 0.005 0.067 877 Dihedral : 4.377 26.796 690 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.22 % Favored : 92.62 % Rotamer: Outliers : 4.28 % Allowed : 30.84 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.37), residues: 623 helix: 1.82 (0.26), residues: 419 sheet: 2.26 (1.51), residues: 10 loop : -1.81 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 128 HIS 0.004 0.001 HIS A 259 PHE 0.020 0.001 PHE A 561 TYR 0.029 0.001 TYR A 215 ARG 0.010 0.000 ARG A 607 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2139.59 seconds wall clock time: 38 minutes 58.35 seconds (2338.35 seconds total)