Starting phenix.real_space_refine on Wed Mar 12 09:44:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sp9_25369/03_2025/7sp9_25369.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sp9_25369/03_2025/7sp9_25369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sp9_25369/03_2025/7sp9_25369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sp9_25369/03_2025/7sp9_25369.map" model { file = "/net/cci-nas-00/data/ceres_data/7sp9_25369/03_2025/7sp9_25369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sp9_25369/03_2025/7sp9_25369.cif" } resolution = 2.9 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= -0.001 sd= 0.828 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1816 atoms to isotropic. 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 35 5.16 5 C 3857 2.51 5 N 984 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5966 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 944 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "C" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 918 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain breaks: 2 Chain: "A" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 4054 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 483} Chain breaks: 1 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'NAG': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.19, per 1000 atoms: 0.70 Number of scatterers: 5966 At special positions: 0 Unit cell: (70.2, 71.28, 154.44, 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 35 16.00 O 1090 8.00 N 984 7.00 C 3857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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: 1.46 Conformation dependent library (CDL) restraints added in 890.5 milliseconds 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1366 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 7 sheets defined 48.8% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.889A pdb=" N THR B 31 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.616A pdb=" N GLY B 65 " --> pdb=" O SER B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.541A pdb=" N TYR B 111 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.620A pdb=" N THR C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'A' and resid 39 through 74 removed outlier: 3.625A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.970A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.559A pdb=" N THR A 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 209 through 221 Proline residue: A 217 - end of helix removed outlier: 3.899A pdb=" N CYS A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 4.044A pdb=" N ARG A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 removed outlier: 5.259A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix removed outlier: 3.514A pdb=" N GLN A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.804A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 356 removed outlier: 5.267A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 392 removed outlier: 4.068A pdb=" N ALA A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 420 Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.616A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 449 removed outlier: 3.834A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix removed outlier: 3.519A pdb=" N MET A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 497 Processing helix chain 'A' and resid 504 through 535 removed outlier: 3.708A pdb=" N ILE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 552 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.572A pdb=" N SER B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 20 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 5.557A pdb=" N GLY B 10 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 5.557A pdb=" N GLY B 10 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.744A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 20 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 52 removed outlier: 4.005A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 34 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR C 115 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 142 through 143 removed outlier: 8.625A pdb=" N ILE A 168 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 116 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE A 170 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N CYS A 118 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLN A 172 " --> pdb=" O CYS A 118 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE A 120 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 84 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG A 115 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 90 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP A 121 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA A 85 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE A 200 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 87 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU A 272 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 10.615A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 873 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: 1.79 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1071 1.33 - 1.45: 1716 1.45 - 1.57: 3260 1.57 - 1.69: 16 1.69 - 1.81: 53 Bond restraints: 6116 Sorted by residual: bond pdb=" CBD Y01 A 902 " pdb=" CBG Y01 A 902 " ideal model delta sigma weight residual 1.520 1.643 -0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" CAV Y01 A 902 " pdb=" CAZ Y01 A 902 " ideal model delta sigma weight residual 1.507 1.612 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" CAV Y01 A 902 " pdb=" CBC Y01 A 902 " ideal model delta sigma weight residual 1.523 1.616 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" CAY Y01 A 902 " pdb=" OAW Y01 A 902 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" CBF Y01 A 902 " pdb=" CBH Y01 A 902 " ideal model delta sigma weight residual 1.550 1.638 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 6111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 8239 2.62 - 5.24: 45 5.24 - 7.87: 14 7.87 - 10.49: 1 10.49 - 13.11: 3 Bond angle restraints: 8302 Sorted by residual: angle pdb=" CAM Y01 A 902 " pdb=" CAY Y01 A 902 " pdb=" OAW Y01 A 902 " ideal model delta sigma weight residual 111.19 124.30 -13.11 3.00e+00 1.11e-01 1.91e+01 angle pdb=" CAI Y01 A 902 " pdb=" CAZ Y01 A 902 " pdb=" CAV Y01 A 902 " ideal model delta sigma weight residual 120.03 131.83 -11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CAZ Y01 A 902 " pdb=" CAV Y01 A 902 " pdb=" CBC Y01 A 902 " ideal model delta sigma weight residual 111.19 122.91 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CAV Y01 A 902 " pdb=" CAZ Y01 A 902 " pdb=" CBH Y01 A 902 " ideal model delta sigma weight residual 116.96 108.74 8.22 3.00e+00 1.11e-01 7.50e+00 angle pdb=" C VAL A 254 " pdb=" N GLU A 255 " pdb=" CA GLU A 255 " ideal model delta sigma weight residual 120.44 116.76 3.68 1.36e+00 5.41e-01 7.31e+00 ... (remaining 8297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 3334 16.23 - 32.47: 207 32.47 - 48.70: 48 48.70 - 64.93: 13 64.93 - 81.16: 5 Dihedral angle restraints: 3607 sinusoidal: 1461 harmonic: 2146 Sorted by residual: dihedral pdb=" CB MET A 382 " pdb=" CG MET A 382 " pdb=" SD MET A 382 " pdb=" CE MET A 382 " ideal model delta sinusoidal sigma weight residual -60.00 -111.24 51.24 3 1.50e+01 4.44e-03 8.99e+00 dihedral pdb=" CA LEU A 293 " pdb=" CB LEU A 293 " pdb=" CG LEU A 293 " pdb=" CD1 LEU A 293 " ideal model delta sinusoidal sigma weight residual 60.00 104.68 -44.68 3 1.50e+01 4.44e-03 8.04e+00 dihedral pdb=" CA ARG A 334 " pdb=" CB ARG A 334 " pdb=" CG ARG A 334 " pdb=" CD ARG A 334 " ideal model delta sinusoidal sigma weight residual -180.00 -137.28 -42.72 3 1.50e+01 4.44e-03 7.67e+00 ... (remaining 3604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 838 0.080 - 0.159: 63 0.159 - 0.239: 2 0.239 - 0.319: 1 0.319 - 0.398: 3 Chirality restraints: 907 Sorted by residual: chirality pdb=" CBG Y01 A 902 " pdb=" CAQ Y01 A 902 " pdb=" CBD Y01 A 902 " pdb=" CBI Y01 A 902 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CBE Y01 A 902 " pdb=" CAP Y01 A 902 " pdb=" CBB Y01 A 902 " pdb=" CBI Y01 A 902 " both_signs ideal model delta sigma weight residual False 2.57 2.93 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CBI Y01 A 902 " pdb=" CAU Y01 A 902 " pdb=" CBE Y01 A 902 " pdb=" CBG Y01 A 902 " both_signs ideal model delta sigma weight residual False 2.94 2.61 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 904 not shown) Planarity restraints: 1026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 94 " 0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO A 95 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 346 " -0.009 2.00e-02 2.50e+03 7.12e-03 1.27e+00 pdb=" CG TRP A 346 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 346 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 346 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 346 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 346 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 346 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 346 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 346 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 346 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 447 " -0.006 2.00e-02 2.50e+03 8.45e-03 1.25e+00 pdb=" CG PHE A 447 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE A 447 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 447 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 447 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 447 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 447 " 0.000 2.00e-02 2.50e+03 ... (remaining 1023 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1081 2.78 - 3.31: 5704 3.31 - 3.84: 9815 3.84 - 4.37: 11047 4.37 - 4.90: 19773 Nonbonded interactions: 47420 Sorted by model distance: nonbonded pdb=" O TYR A 499 " pdb=" OH TYR A 507 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR A 46 " pdb=" OAG Y01 A 902 " model vdw 2.291 3.040 nonbonded pdb=" OG SER C 51 " pdb=" O GLY C 56 " model vdw 2.311 3.040 nonbonded pdb=" O THR A 82 " pdb=" OH TYR A 110 " model vdw 2.322 3.040 nonbonded pdb=" NH2 ARG A 67 " pdb=" O SER A 260 " model vdw 2.323 3.120 ... (remaining 47415 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 18.380 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: 0.010 Load rotamer database and sin/cos tables:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 0.123 6116 Z= 0.291 Angle : 0.568 13.110 8302 Z= 0.260 Chirality : 0.046 0.398 907 Planarity : 0.003 0.029 1026 Dihedral : 12.065 81.163 2238 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.62 (0.31), residues: 725 helix: 2.16 (0.29), residues: 315 sheet: 1.47 (0.44), residues: 150 loop : -0.55 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 346 HIS 0.003 0.001 HIS A 552 PHE 0.019 0.001 PHE A 447 TYR 0.013 0.001 TYR A 414 ARG 0.005 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.602 Fit side-chains REVERT: A 348 ARG cc_start: 0.7565 (mtm110) cc_final: 0.7349 (ptp90) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.9431 time to fit residues: 123.8831 Evaluate side-chains 88 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.106552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.093671 restraints weight = 12328.990| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.06 r_work: 0.3262 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6116 Z= 0.268 Angle : 0.608 8.568 8302 Z= 0.316 Chirality : 0.043 0.131 907 Planarity : 0.004 0.042 1026 Dihedral : 5.440 52.736 917 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.52 % Rotamer: Outliers : 2.23 % Allowed : 12.26 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.30 (0.30), residues: 725 helix: 2.03 (0.29), residues: 311 sheet: 1.14 (0.42), residues: 151 loop : -0.75 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 262 HIS 0.002 0.001 HIS A 174 PHE 0.018 0.002 PHE A 49 TYR 0.015 0.002 TYR A 528 ARG 0.006 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.607 Fit side-chains REVERT: B 66 ARG cc_start: 0.6999 (ttm-80) cc_final: 0.6627 (ttt-90) REVERT: B 84 SER cc_start: 0.8005 (p) cc_final: 0.7669 (t) REVERT: C 28 ILE cc_start: 0.7628 (pt) cc_final: 0.7379 (pt) REVERT: A 248 TYR cc_start: 0.8222 (m-10) cc_final: 0.7873 (m-10) REVERT: A 348 ARG cc_start: 0.8200 (mtm110) cc_final: 0.7797 (ptp90) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 0.9909 time to fit residues: 112.0913 Evaluate side-chains 85 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 552 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN A 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.091403 restraints weight = 12436.000| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.06 r_work: 0.3218 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6116 Z= 0.202 Angle : 0.528 8.472 8302 Z= 0.278 Chirality : 0.042 0.144 907 Planarity : 0.003 0.027 1026 Dihedral : 5.141 42.060 917 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.79 % Favored : 98.07 % Rotamer: Outliers : 3.66 % Allowed : 14.01 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.28 (0.30), residues: 725 helix: 2.08 (0.29), residues: 312 sheet: 0.97 (0.42), residues: 152 loop : -0.75 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 262 HIS 0.002 0.001 HIS A 174 PHE 0.014 0.001 PHE A 249 TYR 0.014 0.001 TYR A 430 ARG 0.007 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.970 Fit side-chains REVERT: B 66 ARG cc_start: 0.6979 (ttm-80) cc_final: 0.6579 (ttt-90) REVERT: A 253 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8311 (m-40) REVERT: A 348 ARG cc_start: 0.8198 (mtm110) cc_final: 0.7769 (ptp90) REVERT: A 372 MET cc_start: 0.7890 (mtp) cc_final: 0.7618 (mtt) REVERT: A 530 ILE cc_start: 0.9014 (tt) cc_final: 0.8531 (pt) REVERT: A 547 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8328 (tp30) outliers start: 23 outliers final: 15 residues processed: 95 average time/residue: 1.6065 time to fit residues: 159.4920 Evaluate side-chains 89 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 552 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 38 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.101309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.089121 restraints weight = 12756.208| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.01 r_work: 0.3216 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6116 Z= 0.252 Angle : 0.547 8.536 8302 Z= 0.295 Chirality : 0.043 0.149 907 Planarity : 0.004 0.038 1026 Dihedral : 4.942 37.930 917 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 4.62 % Allowed : 14.97 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.16 (0.30), residues: 725 helix: 1.99 (0.29), residues: 312 sheet: 0.91 (0.42), residues: 152 loop : -0.85 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.001 0.001 HIS A 195 PHE 0.020 0.002 PHE A 252 TYR 0.014 0.001 TYR A 430 ARG 0.008 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.672 Fit side-chains REVERT: B 66 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6995 (ttt-90) REVERT: B 84 SER cc_start: 0.8247 (p) cc_final: 0.7961 (t) REVERT: A 348 ARG cc_start: 0.8219 (mtm110) cc_final: 0.7742 (ptp90) REVERT: A 372 MET cc_start: 0.7932 (mtp) cc_final: 0.7660 (mtt) outliers start: 29 outliers final: 15 residues processed: 100 average time/residue: 1.0759 time to fit residues: 113.4267 Evaluate side-chains 95 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 552 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 70 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.100834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088787 restraints weight = 12556.041| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.97 r_work: 0.3208 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6116 Z= 0.215 Angle : 0.533 8.999 8302 Z= 0.285 Chirality : 0.042 0.153 907 Planarity : 0.003 0.026 1026 Dihedral : 4.806 35.578 917 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.07 % Favored : 97.79 % Rotamer: Outliers : 3.50 % Allowed : 16.24 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.14 (0.30), residues: 725 helix: 2.00 (0.29), residues: 312 sheet: 0.85 (0.42), residues: 152 loop : -0.86 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 262 HIS 0.002 0.001 HIS A 195 PHE 0.013 0.001 PHE B 47 TYR 0.014 0.001 TYR A 430 ARG 0.005 0.001 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.611 Fit side-chains REVERT: B 66 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6836 (ttt-90) REVERT: C 60 TYR cc_start: 0.8041 (m-80) cc_final: 0.7640 (m-80) REVERT: A 348 ARG cc_start: 0.8143 (mtm110) cc_final: 0.7691 (ttp80) REVERT: A 372 MET cc_start: 0.7984 (mtp) cc_final: 0.7691 (mtt) outliers start: 22 outliers final: 16 residues processed: 96 average time/residue: 1.2637 time to fit residues: 127.7480 Evaluate side-chains 93 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 86 LYS Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 552 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 60 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN A 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.099232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.087448 restraints weight = 12408.428| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.93 r_work: 0.3186 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6116 Z= 0.249 Angle : 0.552 7.506 8302 Z= 0.297 Chirality : 0.043 0.157 907 Planarity : 0.004 0.048 1026 Dihedral : 4.793 37.238 917 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.21 % Favored : 97.66 % Rotamer: Outliers : 3.98 % Allowed : 16.56 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.09 (0.30), residues: 725 helix: 2.03 (0.29), residues: 312 sheet: 0.77 (0.42), residues: 153 loop : -0.94 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 246 HIS 0.001 0.001 HIS A 195 PHE 0.016 0.001 PHE B 47 TYR 0.015 0.001 TYR A 414 ARG 0.010 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.641 Fit side-chains REVERT: B 66 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6915 (ttt-90) REVERT: C 3 GLN cc_start: 0.8457 (mp10) cc_final: 0.8227 (mp10) REVERT: A 348 ARG cc_start: 0.8272 (mtm110) cc_final: 0.7739 (ptp90) REVERT: A 372 MET cc_start: 0.8020 (mtp) cc_final: 0.7731 (mtt) outliers start: 25 outliers final: 17 residues processed: 98 average time/residue: 1.4076 time to fit residues: 145.3137 Evaluate side-chains 98 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 552 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.098584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.086597 restraints weight = 12590.334| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.96 r_work: 0.3171 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6116 Z= 0.255 Angle : 0.572 7.583 8302 Z= 0.305 Chirality : 0.043 0.161 907 Planarity : 0.004 0.028 1026 Dihedral : 4.824 37.700 917 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.52 % Rotamer: Outliers : 3.82 % Allowed : 17.68 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.02 (0.30), residues: 725 helix: 1.97 (0.29), residues: 317 sheet: 0.86 (0.42), residues: 145 loop : -1.08 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.002 0.001 HIS A 195 PHE 0.016 0.002 PHE B 47 TYR 0.015 0.001 TYR A 414 ARG 0.007 0.001 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.777 Fit side-chains REVERT: B 66 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6861 (ttt-90) REVERT: C 3 GLN cc_start: 0.8473 (mp10) cc_final: 0.8220 (mp10) REVERT: A 66 MET cc_start: 0.8727 (mtp) cc_final: 0.8330 (mtt) REVERT: A 348 ARG cc_start: 0.8277 (mtm110) cc_final: 0.7927 (ttp80) REVERT: A 372 MET cc_start: 0.8008 (mtp) cc_final: 0.7723 (mtt) outliers start: 24 outliers final: 16 residues processed: 99 average time/residue: 2.0505 time to fit residues: 213.5443 Evaluate side-chains 100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 552 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.098401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.086454 restraints weight = 12448.563| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.96 r_work: 0.3166 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6116 Z= 0.247 Angle : 0.579 7.695 8302 Z= 0.311 Chirality : 0.043 0.166 907 Planarity : 0.004 0.054 1026 Dihedral : 4.808 40.034 917 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 3.66 % Allowed : 18.47 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.01 (0.30), residues: 725 helix: 2.01 (0.29), residues: 317 sheet: 0.87 (0.42), residues: 145 loop : -1.17 (0.33), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.001 0.001 HIS A 195 PHE 0.016 0.002 PHE B 47 TYR 0.020 0.001 TYR C 60 ARG 0.012 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: B 66 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6830 (ttt-90) REVERT: C 3 GLN cc_start: 0.8448 (mp10) cc_final: 0.8177 (mp10) REVERT: A 348 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7869 (ttp80) REVERT: A 372 MET cc_start: 0.8018 (mtp) cc_final: 0.7742 (mtt) outliers start: 23 outliers final: 14 residues processed: 95 average time/residue: 1.1319 time to fit residues: 113.0715 Evaluate side-chains 90 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 552 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.096782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.084874 restraints weight = 12552.189| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.95 r_work: 0.3141 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6116 Z= 0.303 Angle : 0.611 7.900 8302 Z= 0.330 Chirality : 0.044 0.169 907 Planarity : 0.004 0.056 1026 Dihedral : 5.053 44.911 917 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 2.87 % Allowed : 19.43 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.82 (0.30), residues: 725 helix: 1.89 (0.29), residues: 317 sheet: 0.50 (0.41), residues: 155 loop : -1.19 (0.33), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.002 0.001 HIS A 195 PHE 0.019 0.002 PHE B 47 TYR 0.018 0.002 TYR A 46 ARG 0.009 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.619 Fit side-chains REVERT: B 66 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6850 (ttt-90) REVERT: B 72 ASP cc_start: 0.7578 (t0) cc_final: 0.7301 (OUTLIER) REVERT: C 3 GLN cc_start: 0.8460 (mp10) cc_final: 0.8197 (mp10) REVERT: A 348 ARG cc_start: 0.8248 (mtm110) cc_final: 0.7874 (ttp80) REVERT: A 372 MET cc_start: 0.8138 (mtp) cc_final: 0.7886 (mtt) outliers start: 18 outliers final: 15 residues processed: 92 average time/residue: 1.2054 time to fit residues: 116.6299 Evaluate side-chains 93 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 552 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.098793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086788 restraints weight = 12654.986| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.98 r_work: 0.3179 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6116 Z= 0.191 Angle : 0.573 8.035 8302 Z= 0.307 Chirality : 0.042 0.166 907 Planarity : 0.004 0.029 1026 Dihedral : 4.901 48.322 917 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.21 % Favored : 97.66 % Rotamer: Outliers : 2.07 % Allowed : 20.38 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.97 (0.30), residues: 725 helix: 2.01 (0.29), residues: 317 sheet: 0.70 (0.41), residues: 151 loop : -1.17 (0.34), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.001 0.001 HIS A 360 PHE 0.018 0.001 PHE A 447 TYR 0.018 0.001 TYR A 46 ARG 0.007 0.001 ARG B 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.676 Fit side-chains REVERT: B 66 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6738 (ttt-90) REVERT: C 3 GLN cc_start: 0.8464 (mp10) cc_final: 0.8188 (mp10) REVERT: C 88 GLU cc_start: 0.8417 (pm20) cc_final: 0.8210 (pm20) REVERT: A 348 ARG cc_start: 0.8200 (mtm110) cc_final: 0.7825 (ttp80) REVERT: A 372 MET cc_start: 0.8004 (mtp) cc_final: 0.7717 (mtt) REVERT: A 405 THR cc_start: 0.9001 (m) cc_final: 0.8785 (p) outliers start: 13 outliers final: 10 residues processed: 91 average time/residue: 1.1441 time to fit residues: 109.5696 Evaluate side-chains 91 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 66 ARG Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 552 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.099132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.087145 restraints weight = 12774.648| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.99 r_work: 0.3167 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6116 Z= 0.226 Angle : 0.589 11.836 8302 Z= 0.315 Chirality : 0.043 0.174 907 Planarity : 0.004 0.031 1026 Dihedral : 4.957 50.458 917 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.52 % Rotamer: Outliers : 2.55 % Allowed : 19.75 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.93 (0.30), residues: 725 helix: 1.97 (0.29), residues: 317 sheet: 0.60 (0.41), residues: 153 loop : -1.13 (0.34), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.001 0.001 HIS A 195 PHE 0.018 0.001 PHE A 447 TYR 0.017 0.001 TYR A 46 ARG 0.007 0.001 ARG B 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4555.69 seconds wall clock time: 81 minutes 8.76 seconds (4868.76 seconds total)