Starting phenix.real_space_refine on Thu Mar 6 06:17:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ehx_28154/03_2025/8ehx_28154.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ehx_28154/03_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_28154/03_2025/8ehx_28154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ehx_28154/03_2025/8ehx_28154.map" model { file = "/net/cci-nas-00/data/ceres_data/8ehx_28154/03_2025/8ehx_28154.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ehx_28154/03_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-5624/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: 4.21, per 1000 atoms: 0.82 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: 1.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.58 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: 1.47 Time building geometry restraints manager: 1.60 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: 2.280 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.000 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:4.450 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: 0.7768 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 : 0.745 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: 0.2437 time to fit residues: 32.7443 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 : 0.736 ------------------------------------------------------------------------------- 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 = 0.133801 restraints weight = 7513.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.137933 restraints weight = 3761.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.140506 restraints weight = 2632.761| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.5912 (mtt) REVERT: A 141 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7841 (tmm-80) REVERT: A 258 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8917 (ttpp) REVERT: A 277 ASN cc_start: 0.6769 (t0) cc_final: 0.6516 (t0) REVERT: A 348 LYS cc_start: 0.8758 (mttt) cc_final: 0.8406 (pttt) REVERT: A 584 ASP cc_start: 0.8496 (t0) cc_final: 0.8092 (t0) REVERT: A 592 LEU cc_start: 0.7706 (mt) cc_final: 0.7180 (tt) REVERT: A 613 HIS cc_start: 0.5255 (t-90) cc_final: 0.4938 (m170) REVERT: A 614 GLN cc_start: 0.7309 (pt0) cc_final: 0.6989 (mm-40) REVERT: A 725 LEU cc_start: 0.8236 (mm) cc_final: 0.8036 (mm) outliers start: 23 outliers final: 13 residues processed: 118 average time/residue: 0.1537 time to fit residues: 24.2796 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 : 0.689 ------------------------------------------------------------------------------- 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: 0.0670 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 0.0670 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.0170 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 0.0060 overall best weight: 0.2110 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.187294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.137859 restraints weight = 7621.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142263 restraints weight = 3772.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144937 restraints weight = 2567.728| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5296 Z= 0.157 Angle : 0.537 6.117 7180 Z= 0.283 Chirality : 0.039 0.125 808 Planarity : 0.004 0.061 877 Dihedral : 4.317 26.628 690 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.06 % Favored : 92.62 % Rotamer: Outliers : 4.63 % Allowed : 28.34 % 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: 0.91 (0.36), residues: 623 helix: 1.65 (0.26), residues: 416 sheet: 2.86 (1.72), residues: 10 loop : -1.90 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 485 HIS 0.003 0.001 HIS A 150 PHE 0.010 0.001 PHE A 59 TYR 0.035 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 134 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.5921 (mtt) REVERT: A 348 LYS cc_start: 0.8741 (mttt) cc_final: 0.8418 (pttt) REVERT: A 447 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7957 (t80) REVERT: A 458 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6619 (ptt) REVERT: A 592 LEU cc_start: 0.7314 (mt) cc_final: 0.6920 (tt) REVERT: A 614 GLN cc_start: 0.7284 (pt0) cc_final: 0.6900 (mm-40) REVERT: A 730 PHE cc_start: 0.6916 (t80) cc_final: 0.6533 (t80) outliers start: 26 outliers final: 12 residues processed: 125 average time/residue: 0.1722 time to fit residues: 28.3297 Evaluate side-chains 117 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 158 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 458 MET 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 685 VAL Chi-restraints excluded: chain A residue 732 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.176088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125772 restraints weight = 7851.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129743 restraints weight = 3951.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.132144 restraints weight = 2749.442| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5296 Z= 0.324 Angle : 0.616 5.789 7180 Z= 0.325 Chirality : 0.043 0.188 808 Planarity : 0.005 0.063 877 Dihedral : 4.480 26.943 690 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.90 % Favored : 92.94 % Rotamer: Outliers : 8.20 % Allowed : 24.42 % Favored : 67.38 % 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: 2.38 (1.57), residues: 10 loop : -1.93 (0.49), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 485 HIS 0.007 0.002 HIS A 150 PHE 0.018 0.002 PHE A 521 TYR 0.034 0.002 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 146 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 100 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6725 (tmm) cc_final: 0.5900 (mtt) REVERT: A 225 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.7023 (ttp-170) REVERT: A 348 LYS cc_start: 0.8792 (mttt) cc_final: 0.8432 (pttt) REVERT: A 523 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8104 (tp) REVERT: A 592 LEU cc_start: 0.7416 (mt) cc_final: 0.6928 (tt) REVERT: A 607 ARG cc_start: 0.5080 (ptt-90) cc_final: 0.4558 (ptt-90) REVERT: A 613 HIS cc_start: 0.5577 (t-90) cc_final: 0.5284 (m-70) REVERT: A 619 GLN cc_start: 0.8178 (pt0) cc_final: 0.7273 (pm20) REVERT: A 672 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8203 (pt) REVERT: A 730 PHE cc_start: 0.6777 (t80) cc_final: 0.6452 (t80) outliers start: 46 outliers final: 29 residues processed: 131 average time/residue: 0.2879 time to fit residues: 50.7705 Evaluate side-chains 130 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 167 VAL 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 247 ILE 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 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 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 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: 8.9990 chunk 38 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.178116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.128299 restraints weight = 7645.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132394 restraints weight = 3872.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134760 restraints weight = 2684.984| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2179 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= 0.215 Angle : 0.574 6.468 7180 Z= 0.297 Chirality : 0.041 0.190 808 Planarity : 0.005 0.062 877 Dihedral : 4.443 26.895 690 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.42 % Favored : 93.26 % Rotamer: Outliers : 5.88 % Allowed : 26.02 % Favored : 68.09 % 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: 0.89 (0.36), residues: 623 helix: 1.60 (0.26), residues: 418 sheet: 2.48 (1.58), residues: 10 loop : -1.84 (0.49), residues: 195 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 0.031 0.001 TYR A 215 ARG 0.006 0.000 ARG A 556 *********************** 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 132 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6682 (tmm) cc_final: 0.5933 (mtt) REVERT: A 225 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6605 (ttt180) REVERT: A 348 LYS cc_start: 0.8792 (mttt) cc_final: 0.8448 (pttt) REVERT: A 469 TYR cc_start: 0.8333 (t80) cc_final: 0.8012 (t80) REVERT: A 496 TYR cc_start: 0.8001 (m-80) cc_final: 0.7637 (m-80) REVERT: A 592 LEU cc_start: 0.7333 (mt) cc_final: 0.6886 (tt) REVERT: A 607 ARG cc_start: 0.5031 (ptt-90) cc_final: 0.4615 (ptt-90) REVERT: A 613 HIS cc_start: 0.5579 (t-90) cc_final: 0.5317 (m170) REVERT: A 619 GLN cc_start: 0.8109 (pt0) cc_final: 0.7351 (pm20) REVERT: A 672 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8099 (pt) REVERT: A 730 PHE cc_start: 0.6733 (t80) cc_final: 0.6484 (t80) outliers start: 33 outliers final: 24 residues processed: 125 average time/residue: 0.2192 time to fit residues: 36.2012 Evaluate side-chains 121 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 172 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 ARG 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 498 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 514 THR 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 681 VAL Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 700 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 0.0370 chunk 48 optimal weight: 0.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.177680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.127822 restraints weight = 7773.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.131837 restraints weight = 3910.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.134350 restraints weight = 2710.765| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2374 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= 0.205 Angle : 0.594 11.220 7180 Z= 0.297 Chirality : 0.041 0.241 808 Planarity : 0.005 0.062 877 Dihedral : 4.370 27.028 690 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.10 % Favored : 93.58 % Rotamer: Outliers : 6.24 % Allowed : 26.02 % Favored : 67.74 % 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: 0.98 (0.36), residues: 623 helix: 1.67 (0.26), residues: 418 sheet: 2.49 (1.55), residues: 10 loop : -1.79 (0.49), residues: 195 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 0.009 0.001 PHE A 569 TYR 0.032 0.001 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 132 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6689 (tmm) cc_final: 0.5951 (mtt) REVERT: A 199 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7224 (mmtt) REVERT: A 348 LYS cc_start: 0.8770 (mttt) cc_final: 0.8428 (pttt) REVERT: A 469 TYR cc_start: 0.8302 (t80) cc_final: 0.7992 (t80) REVERT: A 496 TYR cc_start: 0.7986 (m-80) cc_final: 0.7631 (m-80) REVERT: A 523 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8032 (tp) REVERT: A 592 LEU cc_start: 0.7250 (mt) cc_final: 0.6817 (tt) REVERT: A 607 ARG cc_start: 0.5000 (ptt-90) cc_final: 0.4674 (ptt-90) REVERT: A 613 HIS cc_start: 0.5556 (t-90) cc_final: 0.5320 (m170) REVERT: A 614 GLN cc_start: 0.7504 (pt0) cc_final: 0.6718 (mm-40) REVERT: A 619 GLN cc_start: 0.8106 (pt0) cc_final: 0.7377 (pm20) REVERT: A 672 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8113 (pt) outliers start: 35 outliers final: 25 residues processed: 123 average time/residue: 0.2073 time to fit residues: 33.2277 Evaluate side-chains 124 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 158 ILE Chi-restraints excluded: chain A residue 199 LYS 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 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 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 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 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: 0.7980 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.0270 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.177710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127954 restraints weight = 7692.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.131901 restraints weight = 3932.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134418 restraints weight = 2751.833| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5296 Z= 0.199 Angle : 0.580 8.324 7180 Z= 0.294 Chirality : 0.041 0.226 808 Planarity : 0.005 0.065 877 Dihedral : 4.343 27.050 690 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.74 % Favored : 92.94 % Rotamer: Outliers : 6.24 % Allowed : 26.56 % Favored : 67.20 % 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: 1.03 (0.36), residues: 623 helix: 1.72 (0.26), residues: 418 sheet: 2.46 (1.54), residues: 10 loop : -1.80 (0.49), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 485 HIS 0.006 0.001 HIS A 150 PHE 0.009 0.001 PHE A 569 TYR 0.035 0.001 TYR A 215 ARG 0.007 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 133 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6715 (tmm) cc_final: 0.5946 (mtt) REVERT: A 199 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7284 (mmtt) REVERT: A 348 LYS cc_start: 0.8780 (mttt) cc_final: 0.8415 (pttt) REVERT: A 469 TYR cc_start: 0.8310 (t80) cc_final: 0.8016 (t80) REVERT: A 496 TYR cc_start: 0.7985 (m-80) cc_final: 0.7585 (m-80) REVERT: A 523 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7979 (tp) REVERT: A 592 LEU cc_start: 0.7217 (mt) cc_final: 0.6720 (tt) REVERT: A 614 GLN cc_start: 0.7457 (pt0) cc_final: 0.6720 (mm-40) REVERT: A 619 GLN cc_start: 0.8122 (pt0) cc_final: 0.7452 (pm20) outliers start: 35 outliers final: 25 residues processed: 124 average time/residue: 0.2112 time to fit residues: 35.5503 Evaluate side-chains 125 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 199 LYS 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 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 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 560 VAL Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 657 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 49 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 16 optimal weight: 20.0000 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 732 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.174678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.124705 restraints weight = 7724.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.128560 restraints weight = 3966.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.131005 restraints weight = 2779.612| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5296 Z= 0.293 Angle : 0.650 11.575 7180 Z= 0.327 Chirality : 0.044 0.246 808 Planarity : 0.005 0.067 877 Dihedral : 4.530 27.039 690 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.22 % Favored : 92.62 % Rotamer: Outliers : 7.66 % Allowed : 25.31 % 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: 0.91 (0.36), residues: 623 helix: 1.61 (0.26), residues: 418 sheet: 1.99 (1.45), residues: 10 loop : -1.77 (0.50), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 485 HIS 0.011 0.002 HIS A 732 PHE 0.009 0.001 PHE A 697 TYR 0.034 0.002 TYR A 215 ARG 0.010 0.001 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 138 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 95 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6750 (tmm) cc_final: 0.5993 (mtt) REVERT: A 199 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7797 (tttm) REVERT: A 283 PHE cc_start: 0.6958 (m-80) cc_final: 0.6691 (m-80) REVERT: A 348 LYS cc_start: 0.8790 (mttt) cc_final: 0.8429 (pttt) REVERT: A 469 TYR cc_start: 0.8373 (t80) cc_final: 0.8093 (t80) REVERT: A 496 TYR cc_start: 0.8091 (m-80) cc_final: 0.7748 (m-80) REVERT: A 523 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8150 (tp) REVERT: A 592 LEU cc_start: 0.7253 (mt) cc_final: 0.6765 (tt) REVERT: A 619 GLN cc_start: 0.8153 (pt0) cc_final: 0.7446 (pm20) outliers start: 43 outliers final: 33 residues processed: 127 average time/residue: 0.1548 time to fit residues: 25.9114 Evaluate side-chains 126 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 172 ILE Chi-restraints excluded: chain A residue 199 LYS 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 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 458 MET 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 542 ARG 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 681 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 736 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 34 optimal weight: 0.3980 chunk 0 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.178380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.128866 restraints weight = 7737.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132907 restraints weight = 3907.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.135364 restraints weight = 2720.795| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2801 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= 0.185 Angle : 0.625 13.127 7180 Z= 0.308 Chirality : 0.041 0.187 808 Planarity : 0.005 0.067 877 Dihedral : 4.425 27.149 690 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.38 % Favored : 92.46 % Rotamer: Outliers : 4.46 % Allowed : 28.34 % Favored : 67.20 % 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: 1.08 (0.37), residues: 623 helix: 1.73 (0.26), residues: 420 sheet: 2.17 (1.48), residues: 10 loop : -1.72 (0.50), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 128 HIS 0.005 0.001 HIS A 150 PHE 0.008 0.001 PHE A 569 TYR 0.035 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 121 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6699 (tmm) cc_final: 0.5960 (mtt) REVERT: A 283 PHE cc_start: 0.6867 (m-80) cc_final: 0.6545 (m-80) REVERT: A 348 LYS cc_start: 0.8755 (mttt) cc_final: 0.8409 (pttt) REVERT: A 469 TYR cc_start: 0.8303 (t80) cc_final: 0.8023 (t80) REVERT: A 496 TYR cc_start: 0.7996 (m-80) cc_final: 0.7571 (m-80) REVERT: A 523 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7992 (tp) REVERT: A 592 LEU cc_start: 0.7116 (mt) cc_final: 0.6595 (tt) REVERT: A 619 GLN cc_start: 0.8054 (pt0) cc_final: 0.7458 (pm20) REVERT: A 672 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8196 (pt) outliers start: 25 outliers final: 21 residues processed: 116 average time/residue: 0.1723 time to fit residues: 26.1261 Evaluate side-chains 119 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 218 LEU 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 453 ILE Chi-restraints excluded: chain A residue 454 ILE 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 542 ARG 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.0770 chunk 38 optimal weight: 0.0270 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.178939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129022 restraints weight = 7725.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.133028 restraints weight = 3938.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135453 restraints weight = 2759.320| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5296 Z= 0.188 Angle : 0.641 12.686 7180 Z= 0.318 Chirality : 0.042 0.251 808 Planarity : 0.005 0.067 877 Dihedral : 4.387 26.900 690 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.58 % Favored : 93.26 % Rotamer: Outliers : 3.57 % Allowed : 29.59 % Favored : 66.84 % 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: 1.10 (0.36), residues: 623 helix: 1.75 (0.26), residues: 420 sheet: 2.31 (1.49), residues: 10 loop : -1.73 (0.50), residues: 193 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 0.009 0.001 PHE A 569 TYR 0.035 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 117 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6757 (tmm) cc_final: 0.5973 (mtt) REVERT: A 348 LYS cc_start: 0.8774 (mttt) cc_final: 0.8412 (pttt) REVERT: A 469 TYR cc_start: 0.8284 (t80) cc_final: 0.8011 (t80) REVERT: A 496 TYR cc_start: 0.7968 (m-80) cc_final: 0.7585 (m-80) REVERT: A 523 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8008 (tp) REVERT: A 619 GLN cc_start: 0.8050 (pt0) cc_final: 0.7452 (pm20) outliers start: 20 outliers final: 19 residues processed: 113 average time/residue: 0.1936 time to fit residues: 28.3763 Evaluate side-chains 115 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 218 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 453 ILE 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 542 ARG 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 681 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: 0.0970 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 0.0170 overall best weight: 0.5216 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.179743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129985 restraints weight = 7698.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.133980 restraints weight = 3928.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.136107 restraints weight = 2754.252| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5296 Z= 0.185 Angle : 0.637 12.549 7180 Z= 0.315 Chirality : 0.041 0.223 808 Planarity : 0.005 0.067 877 Dihedral : 4.396 26.860 690 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.06 % Favored : 92.78 % Rotamer: Outliers : 3.57 % Allowed : 29.41 % 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: 1.13 (0.36), residues: 623 helix: 1.79 (0.26), residues: 420 sheet: 2.34 (1.52), residues: 10 loop : -1.77 (0.50), residues: 193 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 0.008 0.001 PHE A 569 TYR 0.035 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: 2614.24 seconds wall clock time: 48 minutes 0.03 seconds (2880.03 seconds total)