Starting phenix.real_space_refine on Tue Feb 11 14:17:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smm_40591/02_2025/8smm_40591.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smm_40591/02_2025/8smm_40591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8smm_40591/02_2025/8smm_40591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smm_40591/02_2025/8smm_40591.map" model { file = "/net/cci-nas-00/data/ceres_data/8smm_40591/02_2025/8smm_40591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smm_40591/02_2025/8smm_40591.cif" } resolution = 3.2 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= 0.039 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 47 5.16 5 C 3850 2.51 5 N 962 2.21 5 O 1071 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5930 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 4198 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 14, 'TRANS': 493} Chain breaks: 3 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 937 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 795 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Time building chain proxies: 4.28, per 1000 atoms: 0.72 Number of scatterers: 5930 At special positions: 0 Unit cell: (68.04, 78.84, 140.4, 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 47 16.00 O 1071 8.00 N 962 7.00 C 3850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " 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: 1.48 Conformation dependent library (CDL) restraints added in 858.7 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 50.8% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 23 through 53 Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 57 through 90 removed outlier: 4.373A pdb=" N TYR A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 123 Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 156 removed outlier: 4.124A pdb=" N MET A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.843A pdb=" N VAL A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 230 " --> pdb=" O PHE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 removed outlier: 4.431A pdb=" N ASN A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 302 removed outlier: 3.650A pdb=" N PHE A 302 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 329 removed outlier: 3.630A pdb=" N VAL A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA A 326 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 352 removed outlier: 3.518A pdb=" N LEU A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 394 removed outlier: 3.756A pdb=" N TYR A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 401 through 427 removed outlier: 4.126A pdb=" N THR A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 430 through 457 removed outlier: 3.724A pdb=" N VAL A 434 " --> pdb=" O THR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 465 removed outlier: 3.898A pdb=" N MET A 461 " --> pdb=" O ASN A 458 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A 465 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 474 through 486 Processing helix chain 'A' and resid 505 through 530 removed outlier: 3.963A pdb=" N LEU A 509 " --> pdb=" O PRO A 505 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN A 530 " --> pdb=" O MET A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 568 Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.542A pdb=" N TYR H 35 " --> pdb=" O VAL H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.614A pdb=" N ASP H 93 " --> pdb=" O ARG H 90 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.239A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 163 removed outlier: 6.468A pdb=" N GLY A 161 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N MET A 212 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR A 163 " --> pdb=" O MET A 212 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 105 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY A 313 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLY A 264 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TYR A 263 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 10.805A pdb=" N TYR A 358 " --> pdb=" O TYR A 263 " (cutoff:3.500A) removed outlier: 11.023A pdb=" N ALA A 265 " --> pdb=" O TYR A 358 " (cutoff:3.500A) removed outlier: 11.700A pdb=" N HIS A 360 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 10.435A pdb=" N GLY A 267 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER A 362 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA3, first strand: chain 'H' and resid 14 through 15 Processing sheet with id=AA4, first strand: chain 'H' and resid 61 through 63 removed outlier: 6.762A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG H 101 " --> pdb=" O ASP H 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 61 through 63 removed outlier: 6.762A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR H 120 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 12 through 13 removed outlier: 6.783A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.852A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1014 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: 1.97 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1014 1.33 - 1.45: 1764 1.45 - 1.57: 3235 1.57 - 1.70: 1 1.70 - 1.82: 76 Bond restraints: 6090 Sorted by residual: bond pdb=" N VAL A 52 " pdb=" CA VAL A 52 " ideal model delta sigma weight residual 1.460 1.498 -0.039 1.21e-02 6.83e+03 1.03e+01 bond pdb=" N ILE L 49 " pdb=" CA ILE L 49 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.19e-02 7.06e+03 9.61e+00 bond pdb=" CA SER L 53 " pdb=" CB SER L 53 " ideal model delta sigma weight residual 1.537 1.495 0.042 1.38e-02 5.25e+03 9.12e+00 bond pdb=" N LEU L 48 " pdb=" CA LEU L 48 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.24e-02 6.50e+03 8.17e+00 bond pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.16e+00 ... (remaining 6085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 7995 1.75 - 3.51: 226 3.51 - 5.26: 29 5.26 - 7.02: 3 7.02 - 8.77: 5 Bond angle restraints: 8258 Sorted by residual: angle pdb=" N TRP A 390 " pdb=" CA TRP A 390 " pdb=" C TRP A 390 " ideal model delta sigma weight residual 112.34 104.63 7.71 1.30e+00 5.92e-01 3.52e+01 angle pdb=" CA PHE A 323 " pdb=" CB PHE A 323 " pdb=" CG PHE A 323 " ideal model delta sigma weight residual 113.80 118.50 -4.70 1.00e+00 1.00e+00 2.21e+01 angle pdb=" N ASN A 317 " pdb=" CA ASN A 317 " pdb=" C ASN A 317 " ideal model delta sigma weight residual 111.36 106.39 4.97 1.09e+00 8.42e-01 2.08e+01 angle pdb=" CA PRO A 535 " pdb=" N PRO A 535 " pdb=" CD PRO A 535 " ideal model delta sigma weight residual 112.00 106.00 6.00 1.40e+00 5.10e-01 1.84e+01 angle pdb=" CA SER L 51 " pdb=" C SER L 51 " pdb=" O SER L 51 " ideal model delta sigma weight residual 121.84 117.15 4.69 1.16e+00 7.43e-01 1.63e+01 ... (remaining 8253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3037 17.80 - 35.60: 390 35.60 - 53.40: 87 53.40 - 71.20: 22 71.20 - 89.00: 5 Dihedral angle restraints: 3541 sinusoidal: 1380 harmonic: 2161 Sorted by residual: dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 37.97 55.03 1 1.00e+01 1.00e-02 4.10e+01 dihedral pdb=" CA ILE L 22 " pdb=" CB ILE L 22 " pdb=" CG1 ILE L 22 " pdb=" CD1 ILE L 22 " ideal model delta sinusoidal sigma weight residual 60.00 118.46 -58.46 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU A 462 " pdb=" CA LEU A 462 " pdb=" CB LEU A 462 " pdb=" CG LEU A 462 " ideal model delta sinusoidal sigma weight residual -60.00 -117.61 57.61 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 3538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 640 0.039 - 0.078: 159 0.078 - 0.117: 74 0.117 - 0.156: 13 0.156 - 0.195: 10 Chirality restraints: 896 Sorted by residual: chirality pdb=" CA VAL A 322 " pdb=" N VAL A 322 " pdb=" C VAL A 322 " pdb=" CB VAL A 322 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" CA ARG A 28 " pdb=" N ARG A 28 " pdb=" C ARG A 28 " pdb=" CB ARG A 28 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 893 not shown) Planarity restraints: 1011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 316 " -0.014 2.00e-02 2.50e+03 2.94e-02 8.67e+00 pdb=" C ARG A 316 " 0.051 2.00e-02 2.50e+03 pdb=" O ARG A 316 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN A 317 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 387 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C PHE A 387 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE A 387 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 388 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 343 " -0.234 9.50e-02 1.11e+02 1.05e-01 6.79e+00 pdb=" NE ARG A 343 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 343 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 343 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 343 " -0.007 2.00e-02 2.50e+03 ... (remaining 1008 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1882 2.83 - 3.34: 5214 3.34 - 3.86: 9785 3.86 - 4.38: 10945 4.38 - 4.90: 19698 Nonbonded interactions: 47524 Sorted by model distance: nonbonded pdb=" OG SER A 465 " pdb=" OH TYR A 554 " model vdw 2.307 3.040 nonbonded pdb=" O PHE A 481 " pdb=" OG1 THR A 485 " model vdw 2.328 3.040 nonbonded pdb=" NE2 HIS H 38 " pdb=" OG SER H 102 " model vdw 2.328 3.120 nonbonded pdb=" OG1 THR A 141 " pdb=" OD1 ASP A 144 " model vdw 2.340 3.040 nonbonded pdb=" O LEU A 92 " pdb=" NZ LYS A 255 " model vdw 2.360 3.120 ... (remaining 47519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.360 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.930 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.004 0.088 6090 Z= 0.280 Angle : 0.660 8.770 8258 Z= 0.434 Chirality : 0.046 0.195 896 Planarity : 0.006 0.105 1011 Dihedral : 16.641 88.995 2159 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.31 % Allowed : 22.95 % Favored : 76.74 % 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: 1.25 (0.33), residues: 726 helix: 2.05 (0.30), residues: 323 sheet: 0.26 (0.40), residues: 170 loop : -0.40 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.001 0.000 HIS A 55 PHE 0.018 0.001 PHE A 323 TYR 0.019 0.001 TYR A 471 ARG 0.007 0.001 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: H 87 ASN cc_start: 0.8015 (p0) cc_final: 0.7289 (t0) outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.2203 time to fit residues: 31.1008 Evaluate side-chains 100 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.161205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127756 restraints weight = 6873.707| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.16 r_work: 0.3260 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6090 Z= 0.244 Angle : 0.521 5.198 8258 Z= 0.281 Chirality : 0.041 0.148 896 Planarity : 0.004 0.041 1011 Dihedral : 3.945 47.320 817 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.86 % Allowed : 22.02 % Favored : 76.12 % 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: 1.06 (0.31), residues: 726 helix: 2.01 (0.29), residues: 329 sheet: 0.22 (0.39), residues: 167 loop : -0.81 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.006 0.001 HIS A 344 PHE 0.019 0.001 PHE A 323 TYR 0.014 0.001 TYR A 471 ARG 0.005 0.001 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.703 Fit side-chains REVERT: L 46 LYS cc_start: 0.8495 (tttt) cc_final: 0.8132 (tttp) outliers start: 12 outliers final: 11 residues processed: 109 average time/residue: 0.2092 time to fit residues: 29.1506 Evaluate side-chains 106 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 563 TRP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.157649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124402 restraints weight = 6978.831| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.19 r_work: 0.3202 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6090 Z= 0.267 Angle : 0.527 5.017 8258 Z= 0.285 Chirality : 0.041 0.142 896 Planarity : 0.004 0.044 1011 Dihedral : 3.850 14.592 815 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.33 % Allowed : 23.10 % Favored : 74.57 % 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: 0.83 (0.31), residues: 726 helix: 1.90 (0.28), residues: 328 sheet: -0.11 (0.38), residues: 169 loop : -0.86 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS A 72 PHE 0.022 0.001 PHE A 323 TYR 0.010 0.001 TYR A 562 ARG 0.006 0.001 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.612 Fit side-chains REVERT: A 97 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8532 (mtpp) REVERT: A 283 MET cc_start: 0.9229 (mmp) cc_final: 0.8907 (mmp) REVERT: A 329 ARG cc_start: 0.8302 (mmm-85) cc_final: 0.7502 (mtm110) REVERT: A 561 MET cc_start: 0.7481 (tmm) cc_final: 0.7218 (tmm) REVERT: H 22 ARG cc_start: 0.8188 (ttt-90) cc_final: 0.7555 (mtp-110) REVERT: L 46 LYS cc_start: 0.8534 (tttt) cc_final: 0.8181 (tttp) REVERT: L 103 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8434 (m) outliers start: 15 outliers final: 11 residues processed: 109 average time/residue: 0.2045 time to fit residues: 28.5058 Evaluate side-chains 110 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 563 TRP Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 65 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.161042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.127561 restraints weight = 6960.123| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.96 r_work: 0.3336 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6090 Z= 0.191 Angle : 0.485 5.051 8258 Z= 0.262 Chirality : 0.040 0.128 896 Planarity : 0.004 0.046 1011 Dihedral : 3.695 14.590 815 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.95 % Allowed : 23.10 % Favored : 73.95 % 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: 0.85 (0.31), residues: 726 helix: 1.95 (0.28), residues: 328 sheet: -0.13 (0.39), residues: 169 loop : -0.90 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.003 0.001 HIS A 344 PHE 0.021 0.001 PHE A 323 TYR 0.011 0.001 TYR A 471 ARG 0.006 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.675 Fit side-chains REVERT: A 97 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8443 (mtpp) REVERT: A 283 MET cc_start: 0.9233 (mmp) cc_final: 0.8961 (mmp) REVERT: A 329 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.7310 (mtm110) REVERT: A 407 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7284 (mt-10) REVERT: H 22 ARG cc_start: 0.8188 (ttt-90) cc_final: 0.7752 (mtp-110) REVERT: L 46 LYS cc_start: 0.8456 (tttt) cc_final: 0.8154 (tttp) REVERT: L 103 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8302 (m) outliers start: 19 outliers final: 15 residues processed: 116 average time/residue: 0.2166 time to fit residues: 31.9515 Evaluate side-chains 118 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 563 TRP Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 108 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.160010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126496 restraints weight = 6906.901| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.12 r_work: 0.3188 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6090 Z= 0.245 Angle : 0.516 5.474 8258 Z= 0.278 Chirality : 0.041 0.133 896 Planarity : 0.004 0.046 1011 Dihedral : 3.842 15.302 815 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.57 % Allowed : 22.79 % Favored : 73.64 % 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: 0.73 (0.31), residues: 726 helix: 1.89 (0.28), residues: 328 sheet: -0.30 (0.38), residues: 171 loop : -0.91 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS A 344 PHE 0.022 0.001 PHE A 323 TYR 0.007 0.001 TYR H 98 ARG 0.006 0.001 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.626 Fit side-chains REVERT: A 97 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8465 (mtpp) REVERT: A 283 MET cc_start: 0.9245 (mmp) cc_final: 0.8979 (mmp) REVERT: A 329 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7377 (mtm110) REVERT: A 407 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: L 46 LYS cc_start: 0.8499 (tttt) cc_final: 0.8139 (tttp) REVERT: L 103 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8401 (m) outliers start: 23 outliers final: 19 residues processed: 119 average time/residue: 0.2040 time to fit residues: 31.1686 Evaluate side-chains 118 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 563 TRP Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.160323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128386 restraints weight = 6875.057| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.90 r_work: 0.3319 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6090 Z= 0.206 Angle : 0.496 5.070 8258 Z= 0.267 Chirality : 0.040 0.129 896 Planarity : 0.004 0.046 1011 Dihedral : 3.740 14.772 815 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.72 % Allowed : 22.79 % Favored : 73.49 % 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: 0.77 (0.31), residues: 726 helix: 1.95 (0.28), residues: 328 sheet: -0.29 (0.38), residues: 171 loop : -0.92 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS A 344 PHE 0.021 0.001 PHE A 323 TYR 0.012 0.001 TYR A 471 ARG 0.007 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.641 Fit side-chains REVERT: A 97 LYS cc_start: 0.8775 (mmmt) cc_final: 0.8449 (mtpp) REVERT: A 283 MET cc_start: 0.9221 (mmp) cc_final: 0.8922 (mmp) REVERT: A 329 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7386 (mtm110) REVERT: A 407 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: H 22 ARG cc_start: 0.8178 (ttt-90) cc_final: 0.7576 (mtp-110) REVERT: H 86 MET cc_start: 0.8964 (ptp) cc_final: 0.8755 (mtm) REVERT: L 46 LYS cc_start: 0.8501 (tttt) cc_final: 0.8140 (tttp) REVERT: L 103 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8300 (m) outliers start: 24 outliers final: 19 residues processed: 118 average time/residue: 0.2092 time to fit residues: 31.5024 Evaluate side-chains 118 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 563 TRP Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.157922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125424 restraints weight = 6907.891| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.01 r_work: 0.3296 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6090 Z= 0.285 Angle : 0.544 5.428 8258 Z= 0.293 Chirality : 0.042 0.150 896 Planarity : 0.004 0.045 1011 Dihedral : 3.976 15.589 815 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.03 % Allowed : 22.02 % Favored : 73.95 % 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: 0.62 (0.31), residues: 726 helix: 1.81 (0.28), residues: 328 sheet: -0.44 (0.37), residues: 171 loop : -0.90 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS A 344 PHE 0.022 0.001 PHE A 323 TYR 0.008 0.001 TYR A 427 ARG 0.007 0.001 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.646 Fit side-chains REVERT: A 97 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8454 (mtpp) REVERT: A 283 MET cc_start: 0.9235 (mmp) cc_final: 0.8945 (mmp) REVERT: A 329 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7478 (mtm110) REVERT: A 407 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: H 86 MET cc_start: 0.8984 (ptp) cc_final: 0.8757 (mtm) REVERT: L 46 LYS cc_start: 0.8485 (tttt) cc_final: 0.8130 (tttp) REVERT: L 103 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8478 (m) outliers start: 26 outliers final: 18 residues processed: 118 average time/residue: 0.2172 time to fit residues: 32.4136 Evaluate side-chains 117 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 54 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.161190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128774 restraints weight = 6838.837| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.97 r_work: 0.3339 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6090 Z= 0.203 Angle : 0.504 5.256 8258 Z= 0.271 Chirality : 0.040 0.139 896 Planarity : 0.004 0.046 1011 Dihedral : 3.789 14.840 815 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.19 % Allowed : 22.79 % Favored : 73.02 % 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: 0.72 (0.31), residues: 726 helix: 1.92 (0.28), residues: 328 sheet: -0.39 (0.38), residues: 171 loop : -0.90 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS A 344 PHE 0.021 0.001 PHE A 323 TYR 0.012 0.001 TYR A 471 ARG 0.007 0.001 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.627 Fit side-chains REVERT: A 97 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8393 (mtpp) REVERT: A 283 MET cc_start: 0.9216 (mmp) cc_final: 0.8934 (mmp) REVERT: A 329 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.7360 (mtm110) REVERT: A 407 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: H 86 MET cc_start: 0.8939 (ptp) cc_final: 0.8724 (mtm) REVERT: L 46 LYS cc_start: 0.8445 (tttt) cc_final: 0.8076 (tttp) REVERT: L 103 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8349 (m) outliers start: 27 outliers final: 21 residues processed: 123 average time/residue: 0.2069 time to fit residues: 32.7926 Evaluate side-chains 120 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 563 TRP Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 22 optimal weight: 0.5980 chunk 69 optimal weight: 0.0970 chunk 9 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.131444 restraints weight = 6917.517| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.99 r_work: 0.3377 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6090 Z= 0.154 Angle : 0.498 6.407 8258 Z= 0.262 Chirality : 0.039 0.127 896 Planarity : 0.004 0.047 1011 Dihedral : 3.591 14.846 815 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.10 % Allowed : 24.03 % Favored : 72.87 % 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 (0.31), residues: 726 helix: 2.09 (0.28), residues: 326 sheet: -0.27 (0.38), residues: 170 loop : -0.89 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS A 344 PHE 0.021 0.001 PHE A 323 TYR 0.009 0.001 TYR A 358 ARG 0.007 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.711 Fit side-chains REVERT: A 283 MET cc_start: 0.9227 (mmp) cc_final: 0.8919 (mmp) REVERT: A 329 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.7350 (mtm110) REVERT: H 4 GLU cc_start: 0.7118 (pm20) cc_final: 0.6360 (pt0) REVERT: H 86 MET cc_start: 0.8909 (ptp) cc_final: 0.8708 (mtm) REVERT: L 46 LYS cc_start: 0.8446 (tttt) cc_final: 0.8145 (tttp) REVERT: L 103 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8187 (m) outliers start: 20 outliers final: 17 residues processed: 118 average time/residue: 0.2080 time to fit residues: 31.4069 Evaluate side-chains 114 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.162009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129317 restraints weight = 6882.818| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.97 r_work: 0.3347 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6090 Z= 0.202 Angle : 0.532 7.969 8258 Z= 0.276 Chirality : 0.040 0.132 896 Planarity : 0.004 0.046 1011 Dihedral : 3.682 14.313 815 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.79 % Allowed : 24.65 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.31), residues: 726 helix: 2.00 (0.28), residues: 328 sheet: -0.43 (0.38), residues: 172 loop : -0.90 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS A 72 PHE 0.021 0.001 PHE A 323 TYR 0.012 0.001 TYR A 471 ARG 0.007 0.001 ARG A 374 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.665 Fit side-chains REVERT: A 283 MET cc_start: 0.9231 (mmp) cc_final: 0.8941 (mmp) REVERT: A 329 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7349 (mtm110) REVERT: H 4 GLU cc_start: 0.7133 (pm20) cc_final: 0.6367 (pt0) REVERT: H 86 MET cc_start: 0.8930 (ptp) cc_final: 0.8720 (mtm) REVERT: L 46 LYS cc_start: 0.8467 (tttt) cc_final: 0.8164 (tttp) REVERT: L 103 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8261 (m) outliers start: 18 outliers final: 17 residues processed: 110 average time/residue: 0.2181 time to fit residues: 30.6379 Evaluate side-chains 116 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 92 SER Chi-restraints excluded: chain L residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.0020 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.158895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124124 restraints weight = 6929.029| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.02 r_work: 0.3271 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6090 Z= 0.230 Angle : 0.547 7.937 8258 Z= 0.285 Chirality : 0.041 0.142 896 Planarity : 0.004 0.046 1011 Dihedral : 3.793 14.405 815 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.26 % Allowed : 24.34 % Favored : 72.40 % 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: 0.69 (0.31), residues: 726 helix: 1.92 (0.28), residues: 328 sheet: -0.49 (0.38), residues: 172 loop : -0.89 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS A 344 PHE 0.021 0.001 PHE A 323 TYR 0.008 0.001 TYR A 113 ARG 0.007 0.001 ARG A 374 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3399.72 seconds wall clock time: 61 minutes 7.98 seconds (3667.98 seconds total)