Starting phenix.real_space_refine on Sun Mar 10 21:17:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehx_28154/03_2024/8ehx_28154.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehx_28154/03_2024/8ehx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehx_28154/03_2024/8ehx_28154.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehx_28154/03_2024/8ehx_28154.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehx_28154/03_2024/8ehx_28154.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehx_28154/03_2024/8ehx_28154.pdb" } 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 Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 502": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.59, per 1000 atoms: 0.70 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 - 3.50 Amino acid : False - 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: 1.96 Conformation dependent library (CDL) restraints added in 889.2 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: 0.51 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: 2.13 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: 98.54 - 105.63: 97 105.63 - 112.72: 2771 112.72 - 119.81: 1831 119.81 - 126.90: 2410 126.90 - 133.99: 71 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 2.520 nonbonded pdb=" O MET A 628 " pdb=" OG1 THR A 632 " model vdw 2.215 2.440 nonbonded pdb=" ND2 ASN A 177 " pdb=" O THR A 193 " model vdw 2.263 2.520 nonbonded pdb=" O SER A 603 " pdb=" OG SER A 603 " model vdw 2.267 2.440 nonbonded pdb=" O SER A 60 " pdb=" N ARG A 63 " model vdw 2.299 2.520 ... (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: 1.540 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: 5.750 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.730 Find NCS groups from input model: 0.150 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.210 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.518 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: 0.1764 time to fit residues: 23.1862 Evaluate side-chains 92 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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: 0.0070 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 0.0670 chunk 57 optimal weight: 0.6980 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5296 Z= 0.191 Angle : 0.561 6.641 7180 Z= 0.296 Chirality : 0.040 0.122 808 Planarity : 0.005 0.071 877 Dihedral : 4.500 26.665 690 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.58 % Favored : 93.10 % 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: 0.75 (0.36), residues: 623 helix: 1.51 (0.26), residues: 408 sheet: 2.11 (1.65), residues: 10 loop : -1.73 (0.48), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 485 HIS 0.003 0.001 HIS A 150 PHE 0.011 0.001 PHE A 57 TYR 0.032 0.002 TYR A 215 ARG 0.005 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 135 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.5930 (mtt) REVERT: A 225 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6741 (ttt180) REVERT: A 277 ASN cc_start: 0.6592 (t0) cc_final: 0.6347 (t0) REVERT: A 348 LYS cc_start: 0.8752 (mttt) cc_final: 0.8422 (pttt) REVERT: A 584 ASP cc_start: 0.8483 (t0) cc_final: 0.8094 (t0) REVERT: A 592 LEU cc_start: 0.7667 (mt) cc_final: 0.7107 (tt) outliers start: 35 outliers final: 17 residues processed: 127 average time/residue: 0.1543 time to fit residues: 25.7253 Evaluate side-chains 115 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 172 ILE Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 355 ASN 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 31 optimal weight: 0.0470 chunk 17 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1884 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= 0.179 Angle : 0.536 6.030 7180 Z= 0.280 Chirality : 0.039 0.119 808 Planarity : 0.005 0.063 877 Dihedral : 4.318 26.603 690 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.38 % Favored : 92.46 % Rotamer: Outliers : 6.24 % Allowed : 27.45 % 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: 0.98 (0.36), residues: 623 helix: 1.67 (0.26), residues: 418 sheet: 2.79 (1.69), residues: 10 loop : -1.82 (0.49), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 485 HIS 0.006 0.001 HIS A 259 PHE 0.010 0.001 PHE A 283 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 135 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6613 (tmm) cc_final: 0.6009 (mtt) REVERT: A 197 ASN cc_start: 0.8386 (t0) cc_final: 0.7876 (t0) REVERT: A 283 PHE cc_start: 0.7044 (m-80) cc_final: 0.6843 (m-80) REVERT: A 348 LYS cc_start: 0.8744 (mttt) cc_final: 0.8406 (pttt) REVERT: A 447 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.7955 (t80) REVERT: A 592 LEU cc_start: 0.7329 (mt) cc_final: 0.6922 (tt) REVERT: A 725 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7653 (mm) REVERT: A 730 PHE cc_start: 0.6827 (t80) cc_final: 0.6493 (t80) outliers start: 35 outliers final: 20 residues processed: 123 average time/residue: 0.1414 time to fit residues: 23.6229 Evaluate side-chains 118 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 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 147 ASP Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 355 ASN 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 450 THR Chi-restraints excluded: chain A residue 458 MET 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 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 Chi-restraints excluded: chain A residue 725 LEU 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 56 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 0.0570 chunk 54 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2104 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= 0.178 Angle : 0.545 7.231 7180 Z= 0.278 Chirality : 0.039 0.127 808 Planarity : 0.004 0.063 877 Dihedral : 4.238 26.611 690 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.74 % Favored : 92.94 % Rotamer: Outliers : 8.02 % Allowed : 25.13 % 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: 1.07 (0.36), residues: 623 helix: 1.74 (0.26), residues: 418 sheet: 2.86 (1.67), residues: 10 loop : -1.78 (0.49), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 485 HIS 0.004 0.001 HIS A 259 PHE 0.009 0.001 PHE A 154 TYR 0.033 0.001 TYR A 215 ARG 0.008 0.000 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 fitting. rotamer outliers: 45 poor density : 98 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6676 (tmm) cc_final: 0.6034 (mtt) REVERT: A 197 ASN cc_start: 0.8394 (t0) cc_final: 0.7900 (t0) REVERT: A 225 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6694 (ttt180) REVERT: A 254 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8296 (mm-30) REVERT: A 283 PHE cc_start: 0.6998 (m-80) cc_final: 0.6795 (m-80) REVERT: A 348 LYS cc_start: 0.8748 (mttt) cc_final: 0.8406 (pttt) REVERT: A 447 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.7943 (t80) REVERT: A 469 TYR cc_start: 0.8268 (t80) cc_final: 0.7972 (t80) REVERT: A 523 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.7990 (tp) REVERT: A 592 LEU cc_start: 0.7263 (mt) cc_final: 0.6851 (tt) REVERT: A 607 ARG cc_start: 0.4877 (ptt-90) cc_final: 0.4324 (ptt-90) REVERT: A 619 GLN cc_start: 0.8089 (pt0) cc_final: 0.7453 (pm20) REVERT: A 725 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7610 (mm) REVERT: A 730 PHE cc_start: 0.6777 (t80) cc_final: 0.6474 (t80) outliers start: 45 outliers final: 30 residues processed: 132 average time/residue: 0.1697 time to fit residues: 29.8362 Evaluate side-chains 131 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 97 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 147 ASP 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 227 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 457 THR 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 681 VAL Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 725 LEU 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 50 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2370 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= 0.194 Angle : 0.565 9.315 7180 Z= 0.283 Chirality : 0.040 0.247 808 Planarity : 0.004 0.063 877 Dihedral : 4.222 27.025 690 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.06 % Favored : 92.62 % Rotamer: Outliers : 8.38 % Allowed : 24.24 % 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: 1.13 (0.36), residues: 623 helix: 1.78 (0.26), residues: 419 sheet: 2.76 (1.62), residues: 10 loop : -1.75 (0.50), residues: 194 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 0.009 0.001 PHE A 154 TYR 0.034 0.001 TYR A 215 ARG 0.007 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 145 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 98 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6763 (tmm) cc_final: 0.6042 (mtt) REVERT: A 197 ASN cc_start: 0.8436 (t0) cc_final: 0.7915 (t0) REVERT: A 225 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6700 (ttt180) REVERT: A 348 LYS cc_start: 0.8754 (mttt) cc_final: 0.8395 (pttt) REVERT: A 469 TYR cc_start: 0.8330 (t80) cc_final: 0.8029 (t80) REVERT: A 523 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.7985 (tp) REVERT: A 592 LEU cc_start: 0.7144 (mt) cc_final: 0.6706 (tt) REVERT: A 607 ARG cc_start: 0.4978 (ptt-90) cc_final: 0.4572 (ptt-90) REVERT: A 619 GLN cc_start: 0.8105 (pt0) cc_final: 0.7469 (pm20) REVERT: A 730 PHE cc_start: 0.6758 (t80) cc_final: 0.6544 (t80) outliers start: 47 outliers final: 33 residues processed: 131 average time/residue: 0.1764 time to fit residues: 30.3366 Evaluate side-chains 130 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 95 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 62 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 235 ASP 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 334 GLU Chi-restraints excluded: chain A residue 347 TYR Chi-restraints excluded: chain A residue 355 ASN 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 457 THR 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 628 MET Chi-restraints excluded: chain A residue 657 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 54 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5296 Z= 0.166 Angle : 0.552 7.192 7180 Z= 0.276 Chirality : 0.039 0.135 808 Planarity : 0.004 0.062 877 Dihedral : 4.130 26.598 690 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.74 % Favored : 92.94 % Rotamer: Outliers : 7.49 % Allowed : 25.31 % 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: 1.23 (0.37), residues: 623 helix: 1.85 (0.26), residues: 419 sheet: 2.89 (1.64), residues: 10 loop : -1.71 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 485 HIS 0.010 0.001 HIS A 150 PHE 0.009 0.001 PHE A 154 TYR 0.033 0.001 TYR A 215 ARG 0.005 0.000 ARG A 607 *********************** 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 144 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 102 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6036 (mtt) REVERT: A 197 ASN cc_start: 0.8407 (t0) cc_final: 0.7924 (t0) REVERT: A 225 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6878 (ttt180) REVERT: A 344 LYS cc_start: 0.8841 (mttm) cc_final: 0.8611 (mttm) REVERT: A 348 LYS cc_start: 0.8732 (mttt) cc_final: 0.8383 (pttt) REVERT: A 447 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7930 (t80) REVERT: A 469 TYR cc_start: 0.8277 (t80) cc_final: 0.7951 (t80) REVERT: A 496 TYR cc_start: 0.7963 (m-80) cc_final: 0.7592 (m-80) REVERT: A 523 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.7952 (tp) REVERT: A 592 LEU cc_start: 0.7086 (mt) cc_final: 0.6635 (tt) REVERT: A 607 ARG cc_start: 0.4932 (ptt-90) cc_final: 0.4596 (ptt-90) REVERT: A 619 GLN cc_start: 0.8035 (pt0) cc_final: 0.7480 (pm20) outliers start: 42 outliers final: 28 residues processed: 133 average time/residue: 0.1718 time to fit residues: 29.8064 Evaluate side-chains 131 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 99 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 334 GLU 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 447 PHE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 457 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 38 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5456 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2624 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= 0.176 Angle : 0.582 15.869 7180 Z= 0.285 Chirality : 0.039 0.139 808 Planarity : 0.004 0.063 877 Dihedral : 4.121 26.568 690 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.06 % Favored : 92.62 % Rotamer: Outliers : 7.31 % Allowed : 25.85 % 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: 1.26 (0.37), residues: 623 helix: 1.88 (0.26), residues: 419 sheet: 2.79 (1.63), residues: 10 loop : -1.71 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 485 HIS 0.007 0.001 HIS A 150 PHE 0.010 0.001 PHE A 154 TYR 0.034 0.001 TYR A 215 ARG 0.004 0.000 ARG A 607 *********************** 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 137 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 96 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.6081 (mtt) REVERT: A 197 ASN cc_start: 0.8452 (t0) cc_final: 0.7929 (t0) REVERT: A 225 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6878 (ttt180) REVERT: A 344 LYS cc_start: 0.8843 (mttm) cc_final: 0.8613 (mttm) REVERT: A 348 LYS cc_start: 0.8748 (mttt) cc_final: 0.8398 (pttt) REVERT: A 447 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7930 (t80) REVERT: A 469 TYR cc_start: 0.8293 (t80) cc_final: 0.7979 (t80) REVERT: A 496 TYR cc_start: 0.7960 (m-80) cc_final: 0.7594 (m-80) REVERT: A 523 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.7978 (tp) REVERT: A 619 GLN cc_start: 0.8019 (pt0) cc_final: 0.7546 (pm20) outliers start: 41 outliers final: 30 residues processed: 124 average time/residue: 0.1841 time to fit residues: 29.5378 Evaluate side-chains 128 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 94 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 198 LEU 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 227 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 334 GLU 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 447 PHE 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 457 THR 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 628 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.0000 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 overall best weight: 0.4742 ------------------------------------------------------------------------------- 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 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN A 732 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2808 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= 0.172 Angle : 0.592 15.252 7180 Z= 0.289 Chirality : 0.039 0.151 808 Planarity : 0.005 0.063 877 Dihedral : 4.137 26.484 690 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.22 % Favored : 92.62 % Rotamer: Outliers : 6.77 % Allowed : 25.67 % 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: 1.27 (0.37), residues: 623 helix: 1.90 (0.26), residues: 419 sheet: 2.84 (1.64), residues: 10 loop : -1.74 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 128 HIS 0.011 0.001 HIS A 732 PHE 0.010 0.001 PHE A 154 TYR 0.034 0.001 TYR A 215 ARG 0.009 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 134 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 96 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.6104 (mtt) REVERT: A 197 ASN cc_start: 0.8396 (t0) cc_final: 0.7910 (t0) REVERT: A 206 TRP cc_start: 0.7653 (OUTLIER) cc_final: 0.7380 (m-10) REVERT: A 225 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6917 (ttt180) REVERT: A 283 PHE cc_start: 0.6830 (m-80) cc_final: 0.6596 (m-80) REVERT: A 344 LYS cc_start: 0.8823 (mttm) cc_final: 0.8593 (mttm) REVERT: A 348 LYS cc_start: 0.8742 (mttt) cc_final: 0.8393 (pttt) REVERT: A 447 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7924 (t80) REVERT: A 469 TYR cc_start: 0.8283 (t80) cc_final: 0.7990 (t80) REVERT: A 496 TYR cc_start: 0.7944 (m-80) cc_final: 0.7601 (m-80) REVERT: A 523 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.7984 (tp) REVERT: A 619 GLN cc_start: 0.8009 (pt0) cc_final: 0.7547 (pm20) outliers start: 38 outliers final: 29 residues processed: 121 average time/residue: 0.1892 time to fit residues: 29.5905 Evaluate side-chains 129 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 95 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 361 MET 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 447 PHE 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 457 THR 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 628 MET 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 24 optimal weight: 5.9990 chunk 44 optimal weight: 0.0010 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 53 optimal weight: 0.0170 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 overall best weight: 0.3024 ------------------------------------------------------------------------------- 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 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2991 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= 0.153 Angle : 0.585 14.966 7180 Z= 0.284 Chirality : 0.038 0.149 808 Planarity : 0.005 0.065 877 Dihedral : 4.056 26.385 690 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.06 % Favored : 92.78 % Rotamer: Outliers : 5.88 % Allowed : 26.20 % 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: 1.34 (0.37), residues: 623 helix: 1.98 (0.26), residues: 419 sheet: 2.66 (1.64), residues: 10 loop : -1.77 (0.50), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 128 HIS 0.004 0.001 HIS A 150 PHE 0.010 0.001 PHE A 154 TYR 0.032 0.001 TYR A 215 ARG 0.009 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 134 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 101 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6071 (mtt) REVERT: A 197 ASN cc_start: 0.8336 (t0) cc_final: 0.7874 (t0) REVERT: A 199 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7214 (mmtt) REVERT: A 206 TRP cc_start: 0.7613 (OUTLIER) cc_final: 0.7413 (m-10) REVERT: A 225 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6919 (ttt180) REVERT: A 283 PHE cc_start: 0.6747 (m-80) cc_final: 0.6492 (m-80) REVERT: A 344 LYS cc_start: 0.8819 (mttm) cc_final: 0.8587 (mttm) REVERT: A 348 LYS cc_start: 0.8765 (mttt) cc_final: 0.8435 (pttt) REVERT: A 447 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7944 (t80) REVERT: A 469 TYR cc_start: 0.8211 (t80) cc_final: 0.7924 (t80) REVERT: A 523 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8014 (tp) REVERT: A 614 GLN cc_start: 0.5776 (mm110) cc_final: 0.5563 (mm110) REVERT: A 619 GLN cc_start: 0.7978 (pt0) cc_final: 0.7533 (pm20) REVERT: A 725 LEU cc_start: 0.7986 (mm) cc_final: 0.7773 (mm) outliers start: 33 outliers final: 24 residues processed: 122 average time/residue: 0.1919 time to fit residues: 30.0555 Evaluate side-chains 126 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 96 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 62 LEU 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 225 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 361 MET 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 447 PHE 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 539 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 645 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.0070 chunk 39 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2990 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= 0.182 Angle : 0.598 14.180 7180 Z= 0.290 Chirality : 0.039 0.146 808 Planarity : 0.005 0.067 877 Dihedral : 4.064 26.114 690 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.54 % Favored : 92.30 % Rotamer: Outliers : 5.17 % Allowed : 27.81 % 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: 1.35 (0.37), residues: 623 helix: 1.98 (0.26), residues: 420 sheet: 2.56 (1.60), residues: 10 loop : -1.76 (0.50), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 128 HIS 0.007 0.001 HIS A 150 PHE 0.010 0.001 PHE A 154 TYR 0.033 0.001 TYR A 215 ARG 0.010 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 fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6117 (mtt) REVERT: A 197 ASN cc_start: 0.8335 (t0) cc_final: 0.7821 (t0) REVERT: A 206 TRP cc_start: 0.7652 (OUTLIER) cc_final: 0.7421 (m-10) REVERT: A 225 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6917 (ttt180) REVERT: A 348 LYS cc_start: 0.8765 (mttt) cc_final: 0.8436 (pttt) REVERT: A 447 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7929 (t80) REVERT: A 469 TYR cc_start: 0.8233 (t80) cc_final: 0.7952 (t80) REVERT: A 523 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8042 (tp) REVERT: A 614 GLN cc_start: 0.5656 (mm110) cc_final: 0.5432 (mm110) REVERT: A 619 GLN cc_start: 0.7951 (pt0) cc_final: 0.7539 (pm20) outliers start: 29 outliers final: 20 residues processed: 111 average time/residue: 0.1691 time to fit residues: 24.1608 Evaluate side-chains 119 residues out of total 561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 50 MET 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 225 ARG Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 447 PHE 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 628 MET Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 685 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 477 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.178566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128826 restraints weight = 7659.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132781 restraints weight = 3923.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.135211 restraints weight = 2750.484| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2985 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= 0.226 Angle : 0.611 13.368 7180 Z= 0.301 Chirality : 0.040 0.175 808 Planarity : 0.005 0.067 877 Dihedral : 4.163 26.282 690 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.70 % Favored : 92.13 % Rotamer: Outliers : 4.81 % Allowed : 28.34 % 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: 1.31 (0.37), residues: 623 helix: 1.94 (0.26), residues: 420 sheet: 2.49 (1.59), residues: 10 loop : -1.74 (0.50), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 128 HIS 0.004 0.001 HIS A 739 PHE 0.008 0.001 PHE A 154 TYR 0.033 0.001 TYR A 215 ARG 0.009 0.000 ARG A 607 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1571.96 seconds wall clock time: 29 minutes 0.05 seconds (1740.05 seconds total)