Starting phenix.real_space_refine on Thu Jun 5 10:24:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8smm_40591/06_2025/8smm_40591.cif Found real_map, /net/cci-nas-00/data/ceres_data/8smm_40591/06_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_40591/06_2025/8smm_40591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8smm_40591/06_2025/8smm_40591.map" model { file = "/net/cci-nas-00/data/ceres_data/8smm_40591/06_2025/8smm_40591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8smm_40591/06_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-5710/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: 4.17, per 1000 atoms: 0.70 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: 1.29 Conformation dependent library (CDL) restraints added in 783.1 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: 0.65 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: 1.86 Time building geometry restraints manager: 1.57 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: 2.430 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: 0.050 Process input model: 18.030 Find NCS groups from input model: 0.060 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.570 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.15555 ( 345) hydrogen bonds : angle 5.57550 ( 1014) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.51328 ( 4) covalent geometry : bond 0.00413 ( 6090) covalent geometry : angle 0.65983 ( 8258) *********************** 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 : 0.671 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: 0.2156 time to fit residues: 30.3983 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 : 0.626 ------------------------------------------------------------------------------- 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: 0.6980 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.161339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127942 restraints weight = 6868.340| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.16 r_work: 0.3267 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6092 Z= 0.150 Angle : 0.514 5.129 8262 Z= 0.277 Chirality : 0.041 0.145 896 Planarity : 0.004 0.041 1011 Dihedral : 3.927 46.385 817 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.86 % Allowed : 21.86 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.31), residues: 726 helix: 2.03 (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 0.008 0.001 TRP H 50 HIS 0.007 0.001 HIS A 344 PHE 0.020 0.001 PHE A 323 TYR 0.016 0.001 TYR A 471 ARG 0.005 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 345) hydrogen bonds : angle 4.17016 ( 1014) SS BOND : bond 0.00300 ( 2) SS BOND : angle 0.31350 ( 4) covalent geometry : bond 0.00347 ( 6090) covalent geometry : angle 0.51449 ( 8258) *********************** 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 116 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.679 Fit side-chains REVERT: L 46 LYS cc_start: 0.8490 (tttt) cc_final: 0.8123 (tttp) outliers start: 12 outliers final: 11 residues processed: 111 average time/residue: 0.2419 time to fit residues: 34.8327 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 : 0.809 ------------------------------------------------------------------------------- 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: 0.8980 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.158311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.125168 restraints weight = 6977.245| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.18 r_work: 0.3212 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6092 Z= 0.167 Angle : 0.516 5.056 8262 Z= 0.279 Chirality : 0.041 0.141 896 Planarity : 0.004 0.044 1011 Dihedral : 3.763 14.382 815 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.02 % Allowed : 23.72 % Favored : 74.26 % 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: 1.95 (0.28), residues: 328 sheet: -0.08 (0.38), residues: 169 loop : -0.85 (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 0.023 0.001 PHE A 323 TYR 0.009 0.001 TYR A 562 ARG 0.006 0.001 ARG H 22 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 345) hydrogen bonds : angle 4.25957 ( 1014) SS BOND : bond 0.00306 ( 2) SS BOND : angle 0.47217 ( 4) covalent geometry : bond 0.00386 ( 6090) covalent geometry : angle 0.51580 ( 8258) *********************** 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 116 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.674 Fit side-chains REVERT: L 46 LYS cc_start: 0.8528 (tttt) cc_final: 0.8167 (tttp) REVERT: L 103 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8366 (m) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.2200 time to fit residues: 30.6880 Evaluate side-chains 109 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.157240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.123105 restraints weight = 7040.229| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.04 r_work: 0.3320 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6092 Z= 0.148 Angle : 0.504 5.037 8262 Z= 0.271 Chirality : 0.040 0.131 896 Planarity : 0.004 0.045 1011 Dihedral : 3.761 14.722 815 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.79 % Allowed : 23.72 % 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: 0.80 (0.31), residues: 726 helix: 1.91 (0.28), residues: 328 sheet: -0.19 (0.38), residues: 169 loop : -0.88 (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 0.022 0.001 PHE A 323 TYR 0.011 0.001 TYR A 471 ARG 0.006 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 345) hydrogen bonds : angle 4.21774 ( 1014) SS BOND : bond 0.00346 ( 2) SS BOND : angle 0.56566 ( 4) covalent geometry : bond 0.00341 ( 6090) covalent geometry : angle 0.50354 ( 8258) *********************** 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 121 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.706 Fit side-chains REVERT: A 97 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8492 (mtpp) REVERT: A 329 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.7368 (mtm110) REVERT: H 22 ARG cc_start: 0.8223 (ttt-90) cc_final: 0.7779 (mtp-110) REVERT: L 46 LYS cc_start: 0.8479 (tttt) cc_final: 0.8102 (tttp) REVERT: L 103 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8334 (m) outliers start: 18 outliers final: 14 residues processed: 114 average time/residue: 0.2282 time to fit residues: 33.3738 Evaluate side-chains 113 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 257 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 563 TRP 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 69 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 61 optimal weight: 0.3980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.163509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131280 restraints weight = 6906.537| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.95 r_work: 0.3335 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6092 Z= 0.117 Angle : 0.477 5.049 8262 Z= 0.256 Chirality : 0.039 0.125 896 Planarity : 0.004 0.046 1011 Dihedral : 3.613 14.533 815 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.95 % Allowed : 23.72 % Favored : 73.33 % 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: 2.00 (0.28), residues: 328 sheet: -0.18 (0.39), residues: 169 loop : -0.94 (0.40), residues: 229 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 562 ARG 0.006 0.000 ARG L 67 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 345) hydrogen bonds : angle 4.11060 ( 1014) SS BOND : bond 0.00306 ( 2) SS BOND : angle 0.58999 ( 4) covalent geometry : bond 0.00259 ( 6090) covalent geometry : angle 0.47718 ( 8258) *********************** 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: 19 poor density : 107 time to evaluate : 0.699 Fit side-chains REVERT: A 97 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8444 (mtpp) REVERT: A 113 TYR cc_start: 0.6956 (m-10) cc_final: 0.6751 (m-10) REVERT: A 329 ARG cc_start: 0.8239 (mmm-85) cc_final: 0.7314 (mtm110) REVERT: A 407 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: H 22 ARG cc_start: 0.8229 (ttt-90) cc_final: 0.7634 (mtp-110) REVERT: L 46 LYS cc_start: 0.8485 (tttt) cc_final: 0.8180 (tttp) REVERT: L 103 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8222 (m) outliers start: 19 outliers final: 17 residues processed: 119 average time/residue: 0.2045 time to fit residues: 31.1313 Evaluate side-chains 119 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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 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 63 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.160241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.127743 restraints weight = 6867.438| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.97 r_work: 0.3275 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.004 0.045 6092 Z= 0.164 Angle : 0.525 6.376 8262 Z= 0.282 Chirality : 0.041 0.131 896 Planarity : 0.004 0.046 1011 Dihedral : 3.835 15.158 815 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.57 % Allowed : 23.41 % 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: 0.74 (0.31), residues: 726 helix: 1.91 (0.28), residues: 328 sheet: -0.30 (0.38), residues: 169 loop : -0.93 (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 344 PHE 0.022 0.001 PHE A 323 TYR 0.012 0.001 TYR A 471 ARG 0.007 0.001 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 345) hydrogen bonds : angle 4.29197 ( 1014) SS BOND : bond 0.00320 ( 2) SS BOND : angle 0.62458 ( 4) covalent geometry : bond 0.00383 ( 6090) covalent geometry : angle 0.52489 ( 8258) *********************** 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 123 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.643 Fit side-chains REVERT: A 97 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8476 (mtpp) REVERT: A 329 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.7379 (mtm110) REVERT: A 407 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: L 46 LYS cc_start: 0.8515 (tttt) cc_final: 0.8148 (tttp) REVERT: L 103 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8393 (m) outliers start: 23 outliers final: 16 residues processed: 115 average time/residue: 0.2025 time to fit residues: 29.7911 Evaluate side-chains 113 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.158878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.126890 restraints weight = 6976.341| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.96 r_work: 0.3332 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2389 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= 0.143 Angle : 0.509 6.313 8262 Z= 0.273 Chirality : 0.040 0.130 896 Planarity : 0.004 0.046 1011 Dihedral : 3.764 14.671 815 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.88 % Allowed : 22.48 % 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: 0.74 (0.31), residues: 726 helix: 1.94 (0.28), residues: 328 sheet: -0.32 (0.39), residues: 169 loop : -0.95 (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 344 PHE 0.021 0.001 PHE A 323 TYR 0.011 0.001 TYR A 562 ARG 0.007 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 345) hydrogen bonds : angle 4.23479 ( 1014) SS BOND : bond 0.00319 ( 2) SS BOND : angle 0.63068 ( 4) covalent geometry : bond 0.00329 ( 6090) covalent geometry : angle 0.50936 ( 8258) *********************** 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 125 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.630 Fit side-chains REVERT: A 97 LYS cc_start: 0.8760 (mmmt) cc_final: 0.8400 (mtpp) REVERT: A 274 ASN cc_start: 0.8238 (p0) cc_final: 0.8034 (p0) REVERT: A 329 ARG cc_start: 0.8236 (mmm-85) cc_final: 0.7314 (mtm110) REVERT: A 407 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: L 46 LYS cc_start: 0.8490 (tttt) cc_final: 0.8122 (tttp) REVERT: L 103 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8320 (m) outliers start: 25 outliers final: 21 residues processed: 117 average time/residue: 0.1967 time to fit residues: 29.3956 Evaluate side-chains 119 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 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 67 VAL 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 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 54 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.158714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126750 restraints weight = 6969.197| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.84 r_work: 0.3332 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2463 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= 0.147 Angle : 0.518 6.441 8262 Z= 0.277 Chirality : 0.040 0.137 896 Planarity : 0.004 0.046 1011 Dihedral : 3.782 14.926 815 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.50 % Allowed : 22.33 % Favored : 73.18 % 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: 1.93 (0.28), residues: 328 sheet: -0.38 (0.38), residues: 169 loop : -0.93 (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 344 PHE 0.021 0.001 PHE A 323 TYR 0.012 0.001 TYR A 471 ARG 0.006 0.001 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 345) hydrogen bonds : angle 4.24994 ( 1014) SS BOND : bond 0.00322 ( 2) SS BOND : angle 0.62585 ( 4) covalent geometry : bond 0.00338 ( 6090) covalent geometry : angle 0.51816 ( 8258) *********************** 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 127 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.695 Fit side-chains REVERT: A 97 LYS cc_start: 0.8754 (mmmt) cc_final: 0.8389 (mtpp) REVERT: A 274 ASN cc_start: 0.8262 (p0) cc_final: 0.8037 (p0) REVERT: A 329 ARG cc_start: 0.8265 (mmm-85) cc_final: 0.7380 (mtm110) REVERT: A 407 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: H 86 MET cc_start: 0.8951 (ptp) cc_final: 0.8719 (mtm) REVERT: L 46 LYS cc_start: 0.8495 (tttt) cc_final: 0.8129 (tttp) REVERT: L 103 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8329 (m) outliers start: 29 outliers final: 23 residues processed: 119 average time/residue: 0.2193 time to fit residues: 33.5127 Evaluate side-chains 121 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.0670 chunk 22 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.161941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.130848 restraints weight = 6932.131| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.99 r_work: 0.3351 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6092 Z= 0.131 Angle : 0.517 6.279 8262 Z= 0.273 Chirality : 0.040 0.133 896 Planarity : 0.004 0.045 1011 Dihedral : 3.711 14.629 815 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.03 % Allowed : 23.10 % 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: 0.77 (0.31), residues: 726 helix: 1.97 (0.28), residues: 328 sheet: -0.34 (0.39), residues: 169 loop : -0.92 (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 0.008 0.001 TYR A 146 ARG 0.007 0.001 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 345) hydrogen bonds : angle 4.19678 ( 1014) SS BOND : bond 0.00339 ( 2) SS BOND : angle 0.70166 ( 4) covalent geometry : bond 0.00296 ( 6090) covalent geometry : angle 0.51675 ( 8258) *********************** 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 125 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.671 Fit side-chains REVERT: A 97 LYS cc_start: 0.8722 (mmmt) cc_final: 0.8363 (mtpp) REVERT: A 274 ASN cc_start: 0.8266 (p0) cc_final: 0.8003 (p0) REVERT: A 329 ARG cc_start: 0.8240 (mmm-85) cc_final: 0.7311 (mtm110) REVERT: A 407 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: H 86 MET cc_start: 0.8930 (ptp) cc_final: 0.8691 (mtm) REVERT: L 46 LYS cc_start: 0.8473 (tttt) cc_final: 0.8176 (tttp) REVERT: L 103 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8301 (m) outliers start: 26 outliers final: 22 residues processed: 118 average time/residue: 0.2082 time to fit residues: 31.4450 Evaluate side-chains 120 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 359 THR 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 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 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.156917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.123571 restraints weight = 7023.016| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.93 r_work: 0.3164 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6092 Z= 0.159 Angle : 0.546 7.697 8262 Z= 0.288 Chirality : 0.041 0.142 896 Planarity : 0.004 0.045 1011 Dihedral : 3.840 14.410 815 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.72 % Allowed : 23.10 % Favored : 73.18 % 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: 1.90 (0.28), residues: 328 sheet: -0.44 (0.38), residues: 169 loop : -0.90 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.003 0.001 HIS A 344 PHE 0.022 0.001 PHE A 323 TYR 0.012 0.001 TYR A 471 ARG 0.007 0.001 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 345) hydrogen bonds : angle 4.29444 ( 1014) SS BOND : bond 0.00322 ( 2) SS BOND : angle 0.70796 ( 4) covalent geometry : bond 0.00371 ( 6090) covalent geometry : angle 0.54570 ( 8258) ********************** 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 122 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.703 Fit side-chains REVERT: A 97 LYS cc_start: 0.8766 (mmmt) cc_final: 0.8403 (mtpp) REVERT: A 329 ARG cc_start: 0.8324 (mmm-85) cc_final: 0.7381 (mtm110) REVERT: A 407 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: H 4 GLU cc_start: 0.7420 (pm20) cc_final: 0.6658 (pt0) REVERT: H 86 MET cc_start: 0.8939 (ptp) cc_final: 0.8712 (mtm) REVERT: L 46 LYS cc_start: 0.8505 (tttt) cc_final: 0.8150 (tttp) REVERT: L 103 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8374 (m) outliers start: 24 outliers final: 22 residues processed: 115 average time/residue: 0.2222 time to fit residues: 32.3076 Evaluate side-chains 122 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 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 67 VAL 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 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 0.0000 chunk 40 optimal weight: 0.6980 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.161183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128723 restraints weight = 7024.142| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.01 r_work: 0.3343 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2415 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= 0.123 Angle : 0.514 7.238 8262 Z= 0.270 Chirality : 0.040 0.131 896 Planarity : 0.004 0.045 1011 Dihedral : 3.678 14.574 815 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.88 % Allowed : 23.10 % 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: 0.81 (0.31), residues: 726 helix: 2.05 (0.28), residues: 326 sheet: -0.39 (0.39), residues: 169 loop : -0.88 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS A 344 PHE 0.021 0.001 PHE A 323 TYR 0.008 0.001 TYR A 146 ARG 0.007 0.001 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 345) hydrogen bonds : angle 4.16664 ( 1014) SS BOND : bond 0.00310 ( 2) SS BOND : angle 0.69923 ( 4) covalent geometry : bond 0.00275 ( 6090) covalent geometry : angle 0.51387 ( 8258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3781.10 seconds wall clock time: 66 minutes 30.98 seconds (3990.98 seconds total)