Starting phenix.real_space_refine on Fri Oct 10 13:21:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smm_40591/10_2025/8smm_40591.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smm_40591/10_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_40591/10_2025/8smm_40591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smm_40591/10_2025/8smm_40591.map" model { file = "/net/cci-nas-00/data/ceres_data/8smm_40591/10_2025/8smm_40591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smm_40591/10_2025/8smm_40591.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.46, per 1000 atoms: 0.25 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: 0.51 Conformation dependent library (CDL) restraints added in 243.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.17 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: 0.93 Time building geometry restraints manager: 0.68 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: 2.190 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.400 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.710 ------------------------------------------------------------------------------- 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 6092 Z= 0.286 Angle : 0.660 8.770 8262 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG L 67 TYR 0.019 0.001 TYR A 471 PHE 0.018 0.001 PHE A 323 TRP 0.009 0.001 TRP A 165 HIS 0.001 0.000 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 6090) covalent geometry : angle 0.65983 ( 8258) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.51328 ( 4) hydrogen bonds : bond 0.15555 ( 345) hydrogen bonds : angle 5.57550 ( 1014) *********************** 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 : 0.234 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: 0.0993 time to fit residues: 14.0495 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 : 0.235 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 344 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.156123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.122553 restraints weight = 7044.648| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.14 r_work: 0.3170 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 6092 Z= 0.262 Angle : 0.626 6.326 8262 Z= 0.339 Chirality : 0.045 0.164 896 Planarity : 0.005 0.042 1011 Dihedral : 4.577 55.545 817 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.64 % Allowed : 21.86 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.31), residues: 726 helix: 1.68 (0.28), residues: 327 sheet: -0.10 (0.38), residues: 170 loop : -0.82 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 343 TYR 0.012 0.002 TYR A 471 PHE 0.022 0.002 PHE A 323 TRP 0.013 0.002 TRP H 50 HIS 0.009 0.002 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 6090) covalent geometry : angle 0.62621 ( 8258) SS BOND : bond 0.00300 ( 2) SS BOND : angle 0.82301 ( 4) hydrogen bonds : bond 0.05331 ( 345) hydrogen bonds : angle 4.58974 ( 1014) *********************** 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 121 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.239 Fit side-chains REVERT: H 86 MET cc_start: 0.9034 (ptp) cc_final: 0.8813 (mtm) REVERT: L 46 LYS cc_start: 0.8527 (tttt) cc_final: 0.8170 (tttp) outliers start: 17 outliers final: 11 residues processed: 112 average time/residue: 0.0844 time to fit residues: 12.2690 Evaluate side-chains 109 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 64 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 563 TRP 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 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.160611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.129050 restraints weight = 6927.478| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.84 r_work: 0.3336 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6092 Z= 0.155 Angle : 0.517 5.584 8262 Z= 0.279 Chirality : 0.041 0.137 896 Planarity : 0.004 0.045 1011 Dihedral : 4.329 55.684 817 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.10 % Allowed : 22.02 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.31), residues: 726 helix: 1.86 (0.28), residues: 327 sheet: -0.13 (0.39), residues: 169 loop : -0.85 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 67 TYR 0.013 0.001 TYR A 562 PHE 0.021 0.001 PHE A 323 TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6090) covalent geometry : angle 0.51693 ( 8258) SS BOND : bond 0.00315 ( 2) SS BOND : angle 0.57516 ( 4) hydrogen bonds : bond 0.04363 ( 345) hydrogen bonds : angle 4.28519 ( 1014) *********************** 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 122 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.239 Fit side-chains REVERT: A 97 LYS cc_start: 0.8784 (mmmt) cc_final: 0.8465 (mtpp) REVERT: A 329 ARG cc_start: 0.8258 (mmm-85) cc_final: 0.7450 (mtm110) REVERT: H 86 MET cc_start: 0.8918 (ptp) cc_final: 0.8702 (mtm) REVERT: L 46 LYS cc_start: 0.8477 (tttt) cc_final: 0.8119 (tttp) outliers start: 20 outliers final: 19 residues processed: 117 average time/residue: 0.0896 time to fit residues: 13.2911 Evaluate side-chains 118 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 273 LEU 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 108 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.157972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.127186 restraints weight = 6918.978| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.89 r_work: 0.3304 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6092 Z= 0.207 Angle : 0.561 6.636 8262 Z= 0.304 Chirality : 0.043 0.141 896 Planarity : 0.004 0.046 1011 Dihedral : 4.600 59.057 817 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.31), residues: 726 helix: 1.71 (0.28), residues: 327 sheet: -0.34 (0.38), residues: 169 loop : -0.90 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 67 TYR 0.012 0.001 TYR A 562 PHE 0.022 0.001 PHE A 323 TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 6090) covalent geometry : angle 0.56068 ( 8258) SS BOND : bond 0.00330 ( 2) SS BOND : angle 0.72164 ( 4) hydrogen bonds : bond 0.04776 ( 345) hydrogen bonds : angle 4.47476 ( 1014) *********************** 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 130 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.260 Fit side-chains REVERT: A 97 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8483 (mtpp) REVERT: A 329 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7426 (mtm110) REVERT: A 407 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: A 469 MET cc_start: 0.5684 (ttt) cc_final: 0.5476 (ttt) REVERT: L 46 LYS cc_start: 0.8466 (tttt) cc_final: 0.8112 (tttp) outliers start: 27 outliers final: 21 residues processed: 123 average time/residue: 0.0866 time to fit residues: 13.7127 Evaluate side-chains 123 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 198 MET 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 67 optimal weight: 0.0370 chunk 51 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.159424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125754 restraints weight = 7099.400| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.98 r_work: 0.3183 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6092 Z= 0.131 Angle : 0.498 5.713 8262 Z= 0.268 Chirality : 0.040 0.134 896 Planarity : 0.004 0.047 1011 Dihedral : 4.328 58.478 817 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.41 % Allowed : 24.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.31), residues: 726 helix: 1.87 (0.28), residues: 327 sheet: -0.31 (0.38), residues: 169 loop : -0.91 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 67 TYR 0.012 0.001 TYR A 562 PHE 0.021 0.001 PHE A 323 TRP 0.009 0.001 TRP H 50 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6090) covalent geometry : angle 0.49749 ( 8258) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.69270 ( 4) hydrogen bonds : bond 0.04069 ( 345) hydrogen bonds : angle 4.24065 ( 1014) *********************** 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 127 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.227 Fit side-chains REVERT: A 97 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8472 (mtpp) REVERT: A 113 TYR cc_start: 0.6962 (m-10) cc_final: 0.6706 (m-10) REVERT: A 329 ARG cc_start: 0.8344 (mmm-85) cc_final: 0.7401 (mtm110) REVERT: A 407 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: H 22 ARG cc_start: 0.8210 (ttt-90) cc_final: 0.7623 (mtp-110) REVERT: L 46 LYS cc_start: 0.8488 (tttt) cc_final: 0.8135 (tttp) outliers start: 22 outliers final: 19 residues processed: 120 average time/residue: 0.0773 time to fit residues: 11.8940 Evaluate side-chains 118 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 549 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0370 chunk 54 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.159786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126028 restraints weight = 6976.079| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.96 r_work: 0.3179 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6092 Z= 0.148 Angle : 0.514 6.285 8262 Z= 0.276 Chirality : 0.040 0.138 896 Planarity : 0.004 0.046 1011 Dihedral : 4.374 59.295 817 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.34 % Allowed : 23.57 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.31), residues: 726 helix: 1.85 (0.28), residues: 328 sheet: -0.35 (0.38), residues: 169 loop : -0.94 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 374 TYR 0.012 0.001 TYR A 471 PHE 0.021 0.001 PHE A 323 TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 6090) covalent geometry : angle 0.51416 ( 8258) SS BOND : bond 0.00335 ( 2) SS BOND : angle 0.67765 ( 4) hydrogen bonds : bond 0.04159 ( 345) hydrogen bonds : angle 4.28576 ( 1014) *********************** 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 129 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.190 Fit side-chains REVERT: A 97 LYS cc_start: 0.8796 (mmmt) cc_final: 0.8465 (mtpp) REVERT: A 113 TYR cc_start: 0.7111 (m-10) cc_final: 0.6898 (m-10) REVERT: A 329 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.7420 (mtm110) REVERT: A 407 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: H 101 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8072 (ptt180) REVERT: L 46 LYS cc_start: 0.8508 (tttt) cc_final: 0.8158 (tttp) outliers start: 28 outliers final: 24 residues processed: 121 average time/residue: 0.0912 time to fit residues: 13.9985 Evaluate side-chains 123 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 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 H residue 20 SER Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 101 ARG 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 Chi-restraints excluded: chain L residue 108 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 54 optimal weight: 0.0770 chunk 65 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.160392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126752 restraints weight = 6942.155| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.96 r_work: 0.3156 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6092 Z= 0.135 Angle : 0.505 6.138 8262 Z= 0.270 Chirality : 0.040 0.136 896 Planarity : 0.004 0.047 1011 Dihedral : 4.323 59.702 817 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.81 % Allowed : 22.48 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.31), residues: 726 helix: 1.91 (0.28), residues: 327 sheet: -0.35 (0.38), residues: 169 loop : -0.93 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 374 TYR 0.008 0.001 TYR A 146 PHE 0.021 0.001 PHE A 323 TRP 0.009 0.001 TRP H 50 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6090) covalent geometry : angle 0.50475 ( 8258) SS BOND : bond 0.00331 ( 2) SS BOND : angle 0.66056 ( 4) hydrogen bonds : bond 0.04013 ( 345) hydrogen bonds : angle 4.23587 ( 1014) *********************** 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 134 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.226 Fit side-chains REVERT: A 97 LYS cc_start: 0.8781 (mmmt) cc_final: 0.8449 (mtpp) REVERT: A 113 TYR cc_start: 0.6904 (m-10) cc_final: 0.6669 (m-10) REVERT: A 274 ASN cc_start: 0.8248 (p0) cc_final: 0.8030 (p0) REVERT: A 329 ARG cc_start: 0.8349 (mmm-85) cc_final: 0.7547 (mtm110) REVERT: A 407 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7409 (mt-10) REVERT: H 22 ARG cc_start: 0.8267 (ttt-90) cc_final: 0.7694 (mtp-110) REVERT: H 101 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8049 (ptt180) REVERT: L 46 LYS cc_start: 0.8481 (tttt) cc_final: 0.8118 (tttp) outliers start: 31 outliers final: 27 residues processed: 126 average time/residue: 0.0922 time to fit residues: 14.8280 Evaluate side-chains 127 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 273 LEU Chi-restraints excluded: chain A residue 285 SER 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 517 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 101 ARG 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 Chi-restraints excluded: chain L residue 108 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 0.0970 chunk 57 optimal weight: 0.0970 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.163498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130566 restraints weight = 6841.207| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.93 r_work: 0.3361 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6092 Z= 0.115 Angle : 0.488 5.934 8262 Z= 0.259 Chirality : 0.039 0.131 896 Planarity : 0.004 0.047 1011 Dihedral : 4.200 59.457 817 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.19 % Allowed : 23.57 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.31), residues: 726 helix: 2.01 (0.28), residues: 328 sheet: -0.33 (0.39), residues: 170 loop : -0.93 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 374 TYR 0.012 0.001 TYR A 471 PHE 0.021 0.001 PHE A 323 TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6090) covalent geometry : angle 0.48749 ( 8258) SS BOND : bond 0.00325 ( 2) SS BOND : angle 0.66102 ( 4) hydrogen bonds : bond 0.03724 ( 345) hydrogen bonds : angle 4.12723 ( 1014) *********************** 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 129 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.158 Fit side-chains REVERT: A 97 LYS cc_start: 0.8720 (mmmt) cc_final: 0.8361 (mtpp) REVERT: A 113 TYR cc_start: 0.6900 (m-10) cc_final: 0.6684 (m-10) REVERT: A 407 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: H 22 ARG cc_start: 0.8222 (ttt-90) cc_final: 0.7686 (mtp-110) REVERT: L 46 LYS cc_start: 0.8460 (tttt) cc_final: 0.8161 (tttp) outliers start: 27 outliers final: 23 residues processed: 122 average time/residue: 0.0834 time to fit residues: 13.1174 Evaluate side-chains 121 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 359 THR Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 517 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 60 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.157029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123645 restraints weight = 7051.324| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.88 r_work: 0.3164 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6092 Z= 0.224 Angle : 0.597 7.411 8262 Z= 0.317 Chirality : 0.044 0.160 896 Planarity : 0.004 0.046 1011 Dihedral : 4.552 57.025 817 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.81 % Allowed : 23.26 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.31), residues: 726 helix: 1.72 (0.28), residues: 327 sheet: -0.48 (0.38), residues: 171 loop : -0.95 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 67 TYR 0.009 0.001 TYR H 115 PHE 0.023 0.002 PHE A 323 TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00536 ( 6090) covalent geometry : angle 0.59705 ( 8258) SS BOND : bond 0.00354 ( 2) SS BOND : angle 0.81748 ( 4) hydrogen bonds : bond 0.04684 ( 345) hydrogen bonds : angle 4.48361 ( 1014) *********************** 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 130 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.209 Fit side-chains REVERT: A 97 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8481 (mtpp) REVERT: A 329 ARG cc_start: 0.8321 (mmm-85) cc_final: 0.7343 (mtm110) REVERT: A 407 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: L 46 LYS cc_start: 0.8520 (tttt) cc_final: 0.8183 (tttp) outliers start: 31 outliers final: 26 residues processed: 121 average time/residue: 0.0939 time to fit residues: 14.3746 Evaluate side-chains 124 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 73 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 517 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 5 MET 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 49 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.0670 chunk 2 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.158126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124772 restraints weight = 6927.885| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.06 r_work: 0.3264 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6092 Z= 0.141 Angle : 0.549 7.600 8262 Z= 0.285 Chirality : 0.040 0.144 896 Planarity : 0.004 0.047 1011 Dihedral : 4.360 57.783 817 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.88 % Allowed : 24.34 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.31), residues: 726 helix: 1.79 (0.28), residues: 328 sheet: -0.45 (0.38), residues: 172 loop : -0.90 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 374 TYR 0.012 0.001 TYR A 471 PHE 0.021 0.001 PHE A 323 TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6090) covalent geometry : angle 0.54860 ( 8258) SS BOND : bond 0.00357 ( 2) SS BOND : angle 0.73976 ( 4) hydrogen bonds : bond 0.04072 ( 345) hydrogen bonds : angle 4.30541 ( 1014) ********************** 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 125 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.225 Fit side-chains REVERT: A 97 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8457 (mtpp) REVERT: A 113 TYR cc_start: 0.7061 (m-10) cc_final: 0.6824 (m-10) REVERT: A 329 ARG cc_start: 0.8383 (mmm-85) cc_final: 0.7545 (mtm110) REVERT: A 407 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: L 46 LYS cc_start: 0.8580 (tttt) cc_final: 0.8264 (tttp) outliers start: 25 outliers final: 24 residues processed: 119 average time/residue: 0.0902 time to fit residues: 13.7741 Evaluate side-chains 124 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 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 517 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 41 ARG Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 5 MET 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 30 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.160452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127259 restraints weight = 6889.468| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.04 r_work: 0.3273 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6092 Z= 0.144 Angle : 0.546 7.471 8262 Z= 0.286 Chirality : 0.041 0.141 896 Planarity : 0.004 0.047 1011 Dihedral : 4.333 57.838 817 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.03 % Allowed : 24.19 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.31), residues: 726 helix: 1.79 (0.28), residues: 328 sheet: -0.49 (0.38), residues: 172 loop : -0.90 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 374 TYR 0.007 0.001 TYR A 358 PHE 0.021 0.001 PHE A 323 TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6090) covalent geometry : angle 0.54575 ( 8258) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.71496 ( 4) hydrogen bonds : bond 0.04074 ( 345) hydrogen bonds : angle 4.28909 ( 1014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1689.28 seconds wall clock time: 29 minutes 36.17 seconds (1776.17 seconds total)