Starting phenix.real_space_refine on Sat Feb 17 05:41:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tde_25826/02_2024/7tde_25826.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tde_25826/02_2024/7tde_25826.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tde_25826/02_2024/7tde_25826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tde_25826/02_2024/7tde_25826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tde_25826/02_2024/7tde_25826.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tde_25826/02_2024/7tde_25826.pdb" } 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= 0.001 sd= 0.016 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: 5 Type Number sf(0) Gaussians S 43 5.16 5 C 5915 2.51 5 N 1360 2.21 5 O 1528 1.98 5 H 8888 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 488": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17734 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 10010 Classifications: {'peptide': 605} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 586} Chain breaks: 5 Chain: "B" Number of atoms: 7724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 7724 Classifications: {'peptide': 470} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 455} Chain breaks: 4 Time building chain proxies: 7.84, per 1000 atoms: 0.44 Number of scatterers: 17734 At special positions: 0 Unit cell: (118.57, 98.53, 106.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 O 1528 8.00 N 1360 7.00 C 5915 6.00 H 8888 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 101 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.19 Conformation dependent library (CDL) restraints added in 1.8 seconds 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 86.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 29 through 43 Processing helix chain 'A' and resid 61 through 70 Processing helix chain 'A' and resid 70 through 88 removed outlier: 4.696A pdb=" N ASN A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 138 through 143 removed outlier: 4.019A pdb=" N GLY A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 150 through 173 Processing helix chain 'A' and resid 186 through 199 removed outlier: 4.026A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 238 removed outlier: 5.464A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.612A pdb=" N THR A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.890A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 333 removed outlier: 3.586A pdb=" N GLY A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.766A pdb=" N GLN A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 451 Processing helix chain 'A' and resid 463 through 487 removed outlier: 3.812A pdb=" N ALA A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 494 through 515 Processing helix chain 'A' and resid 530 through 540 removed outlier: 4.061A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA A 536 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 550 through 565 removed outlier: 4.059A pdb=" N PHE A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 565 through 587 Processing helix chain 'A' and resid 597 through 600 Processing helix chain 'A' and resid 601 through 607 Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.696A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 660 removed outlier: 4.411A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 690 Processing helix chain 'B' and resid 17 through 28 Processing helix chain 'B' and resid 29 through 43 Processing helix chain 'B' and resid 61 through 70 Processing helix chain 'B' and resid 70 through 88 removed outlier: 4.732A pdb=" N ASN B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N PHE B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.865A pdb=" N GLU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 95' Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 116 through 137 Processing helix chain 'B' and resid 137 through 143 removed outlier: 4.313A pdb=" N TYR B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY B 143 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 150 through 173 Processing helix chain 'B' and resid 186 through 199 removed outlier: 4.036A pdb=" N VAL B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 238 removed outlier: 3.683A pdb=" N GLY B 211 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLY B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 250 through 263 removed outlier: 3.634A pdb=" N THR B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.679A pdb=" N PHE B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 333 removed outlier: 3.529A pdb=" N LEU B 333 " --> pdb=" O LYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 354 removed outlier: 3.790A pdb=" N LEU B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 396 Processing helix chain 'B' and resid 551 through 587 removed outlier: 3.597A pdb=" N ILE B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Proline residue: B 563 - end of helix Proline residue: B 567 - end of helix Processing helix chain 'B' and resid 597 through 600 Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 615 through 628 Processing helix chain 'B' and resid 632 through 644 removed outlier: 3.633A pdb=" N MET B 636 " --> pdb=" O TRP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 648 through 660 removed outlier: 4.144A pdb=" N PHE B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 690 632 hydrogen bonds defined for protein. 1875 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: 6.63 Time building geometry restraints manager: 13.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 8874 1.03 - 1.23: 31 1.23 - 1.42: 3943 1.42 - 1.62: 5057 1.62 - 1.81: 68 Bond restraints: 17973 Sorted by residual: bond pdb=" CG LEU B 115 " pdb=" CD1 LEU B 115 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.16e+00 bond pdb=" CB MET A 538 " pdb=" CG MET A 538 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.07e+00 bond pdb=" CE2 PHE B 238 " pdb=" CZ PHE B 238 " ideal model delta sigma weight residual 1.382 1.340 0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CB ASN B 614 " pdb=" CG ASN B 614 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" CB ASN A 618 " pdb=" CG ASN A 618 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.68e+00 ... (remaining 17968 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.34: 177 106.34 - 113.28: 20359 113.28 - 120.22: 6744 120.22 - 127.16: 5030 127.16 - 134.09: 97 Bond angle restraints: 32407 Sorted by residual: angle pdb=" N ASP B 269 " pdb=" CA ASP B 269 " pdb=" C ASP B 269 " ideal model delta sigma weight residual 111.33 115.68 -4.35 1.21e+00 6.83e-01 1.30e+01 angle pdb=" N VAL A 270 " pdb=" CA VAL A 270 " pdb=" C VAL A 270 " ideal model delta sigma weight residual 111.89 116.01 -4.12 1.44e+00 4.82e-01 8.17e+00 angle pdb=" CA TYR A 294 " pdb=" CB TYR A 294 " pdb=" CG TYR A 294 " ideal model delta sigma weight residual 113.90 109.12 4.78 1.80e+00 3.09e-01 7.07e+00 angle pdb=" N LEU A 609 " pdb=" CA LEU A 609 " pdb=" C LEU A 609 " ideal model delta sigma weight residual 111.71 114.66 -2.95 1.15e+00 7.56e-01 6.57e+00 angle pdb=" N LEU A 217 " pdb=" CA LEU A 217 " pdb=" C LEU A 217 " ideal model delta sigma weight residual 111.71 114.63 -2.92 1.15e+00 7.56e-01 6.47e+00 ... (remaining 32402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 7829 17.47 - 34.94: 388 34.94 - 52.41: 100 52.41 - 69.87: 150 69.87 - 87.34: 10 Dihedral angle restraints: 8477 sinusoidal: 4383 harmonic: 4094 Sorted by residual: dihedral pdb=" CA MET A 629 " pdb=" C MET A 629 " pdb=" N GLY A 630 " pdb=" CA GLY A 630 " ideal model delta harmonic sigma weight residual 180.00 152.08 27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA SER A 210 " pdb=" C SER A 210 " pdb=" N GLY A 211 " pdb=" CA GLY A 211 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA PHE B 238 " pdb=" C PHE B 238 " pdb=" N GLU B 239 " pdb=" CA GLU B 239 " ideal model delta harmonic sigma weight residual 180.00 -157.57 -22.43 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 8474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 862 0.035 - 0.070: 411 0.070 - 0.104: 103 0.104 - 0.139: 23 0.139 - 0.174: 10 Chirality restraints: 1409 Sorted by residual: chirality pdb=" CA TRP A 271 " pdb=" N TRP A 271 " pdb=" C TRP A 271 " pdb=" CB TRP A 271 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA TYR B 123 " pdb=" N TYR B 123 " pdb=" C TYR B 123 " pdb=" CB TYR B 123 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA TRP B 271 " pdb=" N TRP B 271 " pdb=" C TRP B 271 " pdb=" CB TRP B 271 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 1406 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 497 " 0.053 2.00e-02 2.50e+03 6.55e-02 6.44e+01 pdb=" CG ASN A 497 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 497 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 497 " -0.103 2.00e-02 2.50e+03 pdb="HD21 ASN A 497 " -0.005 2.00e-02 2.50e+03 pdb="HD22 ASN A 497 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 537 " -0.318 9.50e-02 1.11e+02 1.11e-01 3.77e+01 pdb=" NE ARG A 537 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 537 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG A 537 " 0.052 2.00e-02 2.50e+03 pdb=" NH2 ARG A 537 " 0.050 2.00e-02 2.50e+03 pdb="HH11 ARG A 537 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 537 " -0.040 2.00e-02 2.50e+03 pdb="HH21 ARG A 537 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 537 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 618 " -0.029 2.00e-02 2.50e+03 3.53e-02 1.87e+01 pdb=" CG ASN B 618 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B 618 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 618 " 0.056 2.00e-02 2.50e+03 pdb="HD21 ASN B 618 " 0.000 2.00e-02 2.50e+03 pdb="HD22 ASN B 618 " -0.053 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 489 2.14 - 2.76: 33126 2.76 - 3.37: 50371 3.37 - 3.99: 60958 3.99 - 4.60: 98090 Nonbonded interactions: 243034 Sorted by model distance: nonbonded pdb=" HH TYR B 305 " pdb=" OE2 GLU B 673 " model vdw 1.525 1.850 nonbonded pdb=" O THR B 263 " pdb=" HG1 THR B 264 " model vdw 1.536 1.850 nonbonded pdb=" O VAL A 449 " pdb=" HG1 THR A 452 " model vdw 1.553 1.850 nonbonded pdb=" O GLU A 352 " pdb=" HG1 THR A 355 " model vdw 1.576 1.850 nonbonded pdb=" O THR A 263 " pdb=" HG1 THR A 264 " model vdw 1.584 1.850 ... (remaining 243029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.120 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: 0.270 Extract box with map and model: 16.850 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 57.100 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 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 : 0.006 0.059 9085 Z= 0.405 Angle : 0.679 5.046 12354 Z= 0.425 Chirality : 0.043 0.174 1409 Planarity : 0.008 0.104 1508 Dihedral : 12.527 87.342 3173 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.52 % Allowed : 1.56 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.04 (0.25), residues: 1053 helix: -0.04 (0.16), residues: 825 sheet: None (None), residues: 0 loop : 0.96 (0.51), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.005 TRP B 635 HIS 0.013 0.005 HIS A 416 PHE 0.020 0.003 PHE A 248 TYR 0.036 0.006 TYR B 123 ARG 0.012 0.002 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 249 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 TRP cc_start: 0.8097 (p-90) cc_final: 0.7150 (p-90) REVERT: A 95 LYS cc_start: 0.7703 (mmtm) cc_final: 0.7494 (mtpt) REVERT: A 96 ASN cc_start: 0.8306 (t0) cc_final: 0.8029 (p0) REVERT: A 166 ASP cc_start: 0.7157 (t0) cc_final: 0.6729 (m-30) REVERT: A 208 LEU cc_start: 0.8177 (tp) cc_final: 0.7894 (tt) REVERT: A 237 MET cc_start: 0.7523 (ttt) cc_final: 0.7320 (ttp) REVERT: A 294 TYR cc_start: 0.7664 (m-80) cc_final: 0.7457 (m-80) REVERT: A 311 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7328 (mm-40) REVERT: A 314 LYS cc_start: 0.7828 (tttt) cc_final: 0.7600 (tttt) REVERT: A 319 MET cc_start: 0.6141 (tmm) cc_final: 0.5892 (tmm) REVERT: A 322 MET cc_start: 0.7223 (tpp) cc_final: 0.6940 (tpp) REVERT: A 323 LYS cc_start: 0.7587 (tttt) cc_final: 0.7229 (tptm) REVERT: A 326 MET cc_start: 0.7648 (ttm) cc_final: 0.7233 (ttm) REVERT: A 393 GLN cc_start: 0.8544 (mt0) cc_final: 0.8249 (mt0) REVERT: A 421 GLN cc_start: 0.7834 (mp10) cc_final: 0.7599 (mp10) REVERT: A 599 PHE cc_start: 0.7561 (m-80) cc_final: 0.7326 (m-80) REVERT: A 607 ASP cc_start: 0.8146 (t0) cc_final: 0.7633 (t0) REVERT: B 97 PRO cc_start: 0.8644 (Cg_endo) cc_final: 0.8389 (Cg_exo) REVERT: B 126 ILE cc_start: 0.6634 (mt) cc_final: 0.6342 (mt) REVERT: B 132 LEU cc_start: 0.8187 (mt) cc_final: 0.7952 (mt) REVERT: B 136 PHE cc_start: 0.7832 (m-10) cc_final: 0.7555 (m-10) REVERT: B 237 MET cc_start: 0.7939 (ttt) cc_final: 0.7672 (ttp) REVERT: B 258 MET cc_start: 0.8703 (mmt) cc_final: 0.8319 (mmm) REVERT: B 309 LYS cc_start: 0.7952 (tttt) cc_final: 0.7721 (tttt) REVERT: B 312 LEU cc_start: 0.8430 (tp) cc_final: 0.8212 (tt) REVERT: B 321 GLN cc_start: 0.7265 (mt0) cc_final: 0.6860 (mt0) REVERT: B 329 LYS cc_start: 0.8684 (tptt) cc_final: 0.8193 (tptt) REVERT: B 385 LYS cc_start: 0.7482 (tttt) cc_final: 0.7208 (tttt) REVERT: B 673 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7230 (mm-30) REVERT: B 680 ASP cc_start: 0.7524 (m-30) cc_final: 0.7112 (m-30) outliers start: 5 outliers final: 0 residues processed: 252 average time/residue: 0.4819 time to fit residues: 163.0720 Evaluate side-chains 219 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 83 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 0.0170 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9085 Z= 0.273 Angle : 0.540 4.957 12354 Z= 0.300 Chirality : 0.036 0.156 1409 Planarity : 0.004 0.054 1508 Dihedral : 4.546 26.376 1166 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.25 % Allowed : 5.94 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.69 (0.26), residues: 1053 helix: 1.21 (0.17), residues: 824 sheet: None (None), residues: 0 loop : 1.22 (0.50), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 223 HIS 0.001 0.000 HIS B 134 PHE 0.017 0.001 PHE A 501 TYR 0.017 0.002 TYR B 141 ARG 0.003 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 222 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.8265 (t0) cc_final: 0.7931 (t0) REVERT: A 166 ASP cc_start: 0.7150 (t0) cc_final: 0.6670 (m-30) REVERT: A 311 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7316 (mm-40) REVERT: A 314 LYS cc_start: 0.7680 (tttt) cc_final: 0.7453 (tttt) REVERT: A 319 MET cc_start: 0.6303 (tmm) cc_final: 0.6023 (tmm) REVERT: A 322 MET cc_start: 0.7221 (tpp) cc_final: 0.6943 (tpp) REVERT: A 326 MET cc_start: 0.7624 (ttm) cc_final: 0.7249 (ttm) REVERT: A 393 GLN cc_start: 0.8577 (mt0) cc_final: 0.8292 (mt0) REVERT: A 547 ASN cc_start: 0.8439 (m-40) cc_final: 0.8045 (t0) REVERT: A 586 VAL cc_start: 0.8357 (t) cc_final: 0.8117 (m) REVERT: A 599 PHE cc_start: 0.7502 (m-80) cc_final: 0.7277 (m-80) REVERT: A 607 ASP cc_start: 0.8237 (t0) cc_final: 0.7876 (t0) REVERT: B 97 PRO cc_start: 0.8650 (Cg_endo) cc_final: 0.8419 (Cg_exo) REVERT: B 126 ILE cc_start: 0.6571 (mt) cc_final: 0.6279 (mt) REVERT: B 161 VAL cc_start: 0.8751 (p) cc_final: 0.8518 (m) REVERT: B 166 ASP cc_start: 0.8158 (t0) cc_final: 0.7756 (m-30) REVERT: B 258 MET cc_start: 0.8652 (mmt) cc_final: 0.8372 (mmm) REVERT: B 309 LYS cc_start: 0.7898 (tttt) cc_final: 0.7640 (mtpp) REVERT: B 321 GLN cc_start: 0.7279 (mt0) cc_final: 0.6888 (mt0) REVERT: B 329 LYS cc_start: 0.8644 (tptt) cc_final: 0.8104 (tptt) REVERT: B 385 LYS cc_start: 0.7650 (tttt) cc_final: 0.7386 (tttt) REVERT: B 637 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7120 (mm-30) REVERT: B 680 ASP cc_start: 0.7522 (m-30) cc_final: 0.7117 (m-30) outliers start: 12 outliers final: 3 residues processed: 225 average time/residue: 0.4873 time to fit residues: 148.2041 Evaluate side-chains 223 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 219 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 97 optimal weight: 0.0970 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 96 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 631 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9085 Z= 0.237 Angle : 0.499 6.449 12354 Z= 0.273 Chirality : 0.035 0.146 1409 Planarity : 0.004 0.052 1508 Dihedral : 4.230 24.236 1166 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.15 % Allowed : 7.82 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 2.03 (0.26), residues: 1053 helix: 1.46 (0.17), residues: 837 sheet: None (None), residues: 0 loop : 1.26 (0.52), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 223 HIS 0.001 0.001 HIS B 134 PHE 0.016 0.001 PHE A 469 TYR 0.016 0.002 TYR A 256 ARG 0.004 0.000 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 213 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7974 (t80) REVERT: A 111 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6572 (mt-10) REVERT: A 166 ASP cc_start: 0.7135 (t0) cc_final: 0.6625 (m-30) REVERT: A 311 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7385 (mm-40) REVERT: A 314 LYS cc_start: 0.7671 (tttt) cc_final: 0.7452 (tttt) REVERT: A 322 MET cc_start: 0.7257 (tpp) cc_final: 0.6994 (tpp) REVERT: A 326 MET cc_start: 0.7610 (ttm) cc_final: 0.7242 (ttm) REVERT: A 511 GLU cc_start: 0.6762 (pt0) cc_final: 0.6560 (pt0) REVERT: A 586 VAL cc_start: 0.8330 (t) cc_final: 0.8059 (m) REVERT: A 607 ASP cc_start: 0.8284 (t0) cc_final: 0.8025 (t0) REVERT: A 673 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7125 (mm-30) REVERT: A 678 GLU cc_start: 0.7943 (tp30) cc_final: 0.7652 (tm-30) REVERT: B 97 PRO cc_start: 0.8640 (Cg_endo) cc_final: 0.8417 (Cg_exo) REVERT: B 126 ILE cc_start: 0.6624 (mt) cc_final: 0.6335 (mt) REVERT: B 258 MET cc_start: 0.8642 (mmt) cc_final: 0.8399 (mmm) REVERT: B 309 LYS cc_start: 0.7898 (tttt) cc_final: 0.7656 (mtpp) REVERT: B 321 GLN cc_start: 0.7272 (mt0) cc_final: 0.6871 (mt0) REVERT: B 329 LYS cc_start: 0.8632 (tptt) cc_final: 0.8087 (tptt) REVERT: B 385 LYS cc_start: 0.7773 (tttt) cc_final: 0.7448 (tttt) REVERT: B 637 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7047 (mm-30) REVERT: B 648 SER cc_start: 0.8608 (p) cc_final: 0.8298 (m) REVERT: B 656 TYR cc_start: 0.7792 (t80) cc_final: 0.7569 (t80) REVERT: B 680 ASP cc_start: 0.7522 (m-30) cc_final: 0.7118 (m-30) outliers start: 11 outliers final: 4 residues processed: 217 average time/residue: 0.4774 time to fit residues: 141.3559 Evaluate side-chains 216 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 210 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 97 optimal weight: 0.4980 chunk 103 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9085 Z= 0.228 Angle : 0.476 4.410 12354 Z= 0.263 Chirality : 0.034 0.147 1409 Planarity : 0.004 0.052 1508 Dihedral : 4.051 23.140 1166 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.04 % Allowed : 8.24 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 2.28 (0.26), residues: 1053 helix: 1.65 (0.17), residues: 836 sheet: None (None), residues: 0 loop : 1.30 (0.52), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 223 HIS 0.003 0.001 HIS B 134 PHE 0.013 0.001 PHE A 501 TYR 0.015 0.002 TYR A 256 ARG 0.003 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 215 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6553 (mt-10) REVERT: A 166 ASP cc_start: 0.7153 (t0) cc_final: 0.6598 (m-30) REVERT: A 311 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7373 (mm-40) REVERT: A 322 MET cc_start: 0.7227 (tpp) cc_final: 0.6947 (tpp) REVERT: A 326 MET cc_start: 0.7616 (ttm) cc_final: 0.7248 (ttm) REVERT: A 547 ASN cc_start: 0.8457 (t0) cc_final: 0.8192 (t0) REVERT: A 586 VAL cc_start: 0.8412 (t) cc_final: 0.8163 (m) REVERT: A 607 ASP cc_start: 0.8298 (t0) cc_final: 0.8029 (t0) REVERT: A 678 GLU cc_start: 0.7934 (tp30) cc_final: 0.7664 (tm-30) REVERT: B 126 ILE cc_start: 0.6648 (mt) cc_final: 0.6351 (mt) REVERT: B 166 ASP cc_start: 0.8046 (t0) cc_final: 0.7810 (m-30) REVERT: B 258 MET cc_start: 0.8624 (mmt) cc_final: 0.8410 (mmm) REVERT: B 309 LYS cc_start: 0.7907 (tttt) cc_final: 0.7647 (mtpp) REVERT: B 321 GLN cc_start: 0.7262 (mt0) cc_final: 0.6857 (mt0) REVERT: B 329 LYS cc_start: 0.8667 (tptt) cc_final: 0.8146 (tptt) REVERT: B 385 LYS cc_start: 0.7832 (tttt) cc_final: 0.7525 (tttt) REVERT: B 637 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7000 (mm-30) REVERT: B 648 SER cc_start: 0.8617 (p) cc_final: 0.8339 (m) REVERT: B 656 TYR cc_start: 0.7797 (t80) cc_final: 0.7565 (t80) REVERT: B 680 ASP cc_start: 0.7518 (m-30) cc_final: 0.7120 (m-30) outliers start: 10 outliers final: 5 residues processed: 218 average time/residue: 0.4728 time to fit residues: 140.3302 Evaluate side-chains 218 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 212 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9085 Z= 0.382 Angle : 0.525 6.364 12354 Z= 0.294 Chirality : 0.037 0.160 1409 Planarity : 0.004 0.054 1508 Dihedral : 4.171 24.954 1166 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.25 % Allowed : 9.59 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.96 (0.26), residues: 1053 helix: 1.43 (0.17), residues: 837 sheet: None (None), residues: 0 loop : 1.17 (0.53), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 223 HIS 0.003 0.001 HIS B 134 PHE 0.017 0.001 PHE A 195 TYR 0.015 0.002 TYR B 141 ARG 0.004 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 216 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 TYR cc_start: 0.8552 (t80) cc_final: 0.7568 (t80) REVERT: A 166 ASP cc_start: 0.7162 (t0) cc_final: 0.6624 (m-30) REVERT: A 311 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7435 (mm-40) REVERT: A 322 MET cc_start: 0.7262 (tpp) cc_final: 0.6987 (tpp) REVERT: A 326 MET cc_start: 0.7662 (ttm) cc_final: 0.7361 (ttm) REVERT: A 586 VAL cc_start: 0.8426 (t) cc_final: 0.8182 (m) REVERT: A 595 ASN cc_start: 0.8100 (t0) cc_final: 0.7847 (t0) REVERT: A 607 ASP cc_start: 0.8308 (t0) cc_final: 0.8050 (t0) REVERT: A 678 GLU cc_start: 0.7941 (tp30) cc_final: 0.7656 (tm-30) REVERT: B 136 PHE cc_start: 0.7862 (m-10) cc_final: 0.7562 (m-10) REVERT: B 309 LYS cc_start: 0.7917 (tttt) cc_final: 0.7636 (mtpp) REVERT: B 321 GLN cc_start: 0.7291 (mt0) cc_final: 0.6882 (mt0) REVERT: B 329 LYS cc_start: 0.8640 (tptt) cc_final: 0.8103 (tptt) REVERT: B 637 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7060 (mm-30) REVERT: B 648 SER cc_start: 0.8607 (p) cc_final: 0.8335 (m) REVERT: B 656 TYR cc_start: 0.7824 (t80) cc_final: 0.7598 (t80) REVERT: B 680 ASP cc_start: 0.7521 (m-30) cc_final: 0.7124 (m-30) outliers start: 12 outliers final: 10 residues processed: 219 average time/residue: 0.4745 time to fit residues: 141.1239 Evaluate side-chains 228 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 217 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 103 optimal weight: 0.2980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9085 Z= 0.274 Angle : 0.484 5.043 12354 Z= 0.268 Chirality : 0.035 0.144 1409 Planarity : 0.004 0.053 1508 Dihedral : 4.030 22.929 1166 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.46 % Allowed : 9.28 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 2.15 (0.26), residues: 1053 helix: 1.60 (0.17), residues: 829 sheet: None (None), residues: 0 loop : 1.06 (0.50), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 223 HIS 0.003 0.001 HIS B 134 PHE 0.014 0.001 PHE A 499 TYR 0.016 0.002 TYR A 123 ARG 0.004 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 216 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 TYR cc_start: 0.8521 (t80) cc_final: 0.7525 (t80) REVERT: A 111 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6655 (mt-10) REVERT: A 166 ASP cc_start: 0.7162 (t0) cc_final: 0.6588 (m-30) REVERT: A 322 MET cc_start: 0.7224 (tpp) cc_final: 0.6938 (tpp) REVERT: A 326 MET cc_start: 0.7628 (ttm) cc_final: 0.7339 (ttm) REVERT: A 537 ARG cc_start: 0.7351 (ttm170) cc_final: 0.7043 (ttm170) REVERT: A 547 ASN cc_start: 0.8340 (t0) cc_final: 0.8119 (t0) REVERT: A 586 VAL cc_start: 0.8412 (t) cc_final: 0.8161 (m) REVERT: A 607 ASP cc_start: 0.8314 (t0) cc_final: 0.8053 (t0) REVERT: A 678 GLU cc_start: 0.7953 (tp30) cc_final: 0.7648 (tm-30) REVERT: B 136 PHE cc_start: 0.7867 (m-10) cc_final: 0.7555 (m-10) REVERT: B 166 ASP cc_start: 0.8068 (t0) cc_final: 0.7813 (m-30) REVERT: B 309 LYS cc_start: 0.7872 (tttt) cc_final: 0.7654 (mtpp) REVERT: B 321 GLN cc_start: 0.7273 (mt0) cc_final: 0.6859 (mt0) REVERT: B 329 LYS cc_start: 0.8664 (tptt) cc_final: 0.8104 (tptt) REVERT: B 385 LYS cc_start: 0.7851 (tttt) cc_final: 0.7555 (tttt) REVERT: B 637 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.7037 (mm-30) REVERT: B 648 SER cc_start: 0.8616 (p) cc_final: 0.8355 (m) REVERT: B 656 TYR cc_start: 0.7823 (t80) cc_final: 0.7593 (t80) REVERT: B 680 ASP cc_start: 0.7511 (m-30) cc_final: 0.7108 (m-30) outliers start: 14 outliers final: 10 residues processed: 221 average time/residue: 0.5040 time to fit residues: 152.1233 Evaluate side-chains 223 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 212 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9085 Z= 0.383 Angle : 0.526 6.708 12354 Z= 0.295 Chirality : 0.037 0.155 1409 Planarity : 0.004 0.054 1508 Dihedral : 4.162 23.744 1166 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.56 % Allowed : 9.80 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 1.80 (0.26), residues: 1053 helix: 1.38 (0.17), residues: 829 sheet: None (None), residues: 0 loop : 0.84 (0.50), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 223 HIS 0.003 0.001 HIS B 134 PHE 0.027 0.001 PHE A 499 TYR 0.016 0.002 TYR A 651 ARG 0.004 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 216 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6688 (mt-10) REVERT: A 166 ASP cc_start: 0.7167 (t0) cc_final: 0.6669 (m-30) REVERT: A 186 ILE cc_start: 0.8305 (tp) cc_final: 0.8073 (mt) REVERT: A 278 SER cc_start: 0.8767 (t) cc_final: 0.8289 (p) REVERT: A 322 MET cc_start: 0.7254 (tpp) cc_final: 0.6981 (tpp) REVERT: A 326 MET cc_start: 0.7640 (ttm) cc_final: 0.7351 (ttm) REVERT: A 537 ARG cc_start: 0.7408 (ttm170) cc_final: 0.7084 (ttm170) REVERT: A 586 VAL cc_start: 0.8426 (t) cc_final: 0.8182 (m) REVERT: A 595 ASN cc_start: 0.8149 (t0) cc_final: 0.7907 (t0) REVERT: A 607 ASP cc_start: 0.8310 (t0) cc_final: 0.8056 (t0) REVERT: A 678 GLU cc_start: 0.7950 (tp30) cc_final: 0.7644 (tm-30) REVERT: B 136 PHE cc_start: 0.7879 (m-10) cc_final: 0.7594 (m-10) REVERT: B 166 ASP cc_start: 0.8097 (t0) cc_final: 0.7817 (m-30) REVERT: B 309 LYS cc_start: 0.7929 (tttt) cc_final: 0.7655 (mtpp) REVERT: B 321 GLN cc_start: 0.7297 (mt0) cc_final: 0.6898 (mt0) REVERT: B 329 LYS cc_start: 0.8677 (tptt) cc_final: 0.8119 (tptt) REVERT: B 637 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7088 (mm-30) REVERT: B 648 SER cc_start: 0.8608 (p) cc_final: 0.8338 (m) REVERT: B 680 ASP cc_start: 0.7512 (m-30) cc_final: 0.7114 (m-30) outliers start: 15 outliers final: 11 residues processed: 220 average time/residue: 0.5339 time to fit residues: 163.0072 Evaluate side-chains 226 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 214 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.1980 chunk 19 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.1980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9085 Z= 0.179 Angle : 0.459 5.149 12354 Z= 0.251 Chirality : 0.034 0.144 1409 Planarity : 0.003 0.053 1508 Dihedral : 3.903 20.405 1166 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.04 % Allowed : 10.74 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 2.33 (0.26), residues: 1053 helix: 1.76 (0.17), residues: 829 sheet: None (None), residues: 0 loop : 0.98 (0.50), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 223 HIS 0.003 0.001 HIS B 134 PHE 0.017 0.001 PHE A 499 TYR 0.014 0.001 TYR A 256 ARG 0.004 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 213 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 TYR cc_start: 0.8518 (t80) cc_final: 0.7493 (t80) REVERT: A 111 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6642 (mt-10) REVERT: A 166 ASP cc_start: 0.7161 (t0) cc_final: 0.6608 (m-30) REVERT: A 186 ILE cc_start: 0.8217 (tp) cc_final: 0.7957 (mt) REVERT: A 322 MET cc_start: 0.7196 (tpp) cc_final: 0.6914 (tpp) REVERT: A 326 MET cc_start: 0.7611 (ttm) cc_final: 0.7312 (ttm) REVERT: A 537 ARG cc_start: 0.7387 (ttm170) cc_final: 0.7087 (ttm170) REVERT: A 586 VAL cc_start: 0.8407 (t) cc_final: 0.8153 (m) REVERT: A 607 ASP cc_start: 0.8324 (t0) cc_final: 0.8064 (t0) REVERT: A 678 GLU cc_start: 0.7942 (tp30) cc_final: 0.7651 (tm-30) REVERT: B 136 PHE cc_start: 0.7850 (m-10) cc_final: 0.7550 (m-10) REVERT: B 166 ASP cc_start: 0.8046 (t0) cc_final: 0.7789 (m-30) REVERT: B 309 LYS cc_start: 0.7887 (tttt) cc_final: 0.7639 (mtpp) REVERT: B 321 GLN cc_start: 0.7299 (mt0) cc_final: 0.6920 (mt0) REVERT: B 329 LYS cc_start: 0.8653 (tptt) cc_final: 0.8107 (tptt) REVERT: B 637 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.7024 (mm-30) REVERT: B 648 SER cc_start: 0.8633 (p) cc_final: 0.8372 (m) REVERT: B 680 ASP cc_start: 0.7497 (m-30) cc_final: 0.7107 (m-30) outliers start: 10 outliers final: 8 residues processed: 217 average time/residue: 0.4694 time to fit residues: 138.5135 Evaluate side-chains 222 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 213 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 98 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 0.0070 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 95 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9085 Z= 0.225 Angle : 0.467 6.814 12354 Z= 0.256 Chirality : 0.034 0.145 1409 Planarity : 0.003 0.049 1508 Dihedral : 3.855 20.042 1166 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.25 % Allowed : 10.53 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 2.45 (0.26), residues: 1053 helix: 1.85 (0.17), residues: 830 sheet: None (None), residues: 0 loop : 1.03 (0.50), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 223 HIS 0.003 0.001 HIS B 134 PHE 0.019 0.001 PHE A 499 TYR 0.015 0.001 TYR A 256 ARG 0.006 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 213 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6636 (mt-10) REVERT: A 166 ASP cc_start: 0.7179 (t0) cc_final: 0.6614 (m-30) REVERT: A 186 ILE cc_start: 0.8234 (tp) cc_final: 0.7970 (mt) REVERT: A 322 MET cc_start: 0.7198 (tpp) cc_final: 0.6932 (tpp) REVERT: A 326 MET cc_start: 0.7602 (ttm) cc_final: 0.7333 (ttm) REVERT: A 537 ARG cc_start: 0.7370 (ttm170) cc_final: 0.7073 (ttm170) REVERT: A 607 ASP cc_start: 0.8311 (t0) cc_final: 0.8059 (t0) REVERT: A 678 GLU cc_start: 0.7940 (tp30) cc_final: 0.7668 (tm-30) REVERT: B 136 PHE cc_start: 0.7855 (m-10) cc_final: 0.7579 (m-10) REVERT: B 166 ASP cc_start: 0.8032 (t0) cc_final: 0.7784 (m-30) REVERT: B 309 LYS cc_start: 0.7912 (tttt) cc_final: 0.7623 (mtpp) REVERT: B 321 GLN cc_start: 0.7303 (mt0) cc_final: 0.6923 (mt0) REVERT: B 329 LYS cc_start: 0.8655 (tptt) cc_final: 0.8335 (tptt) REVERT: B 385 LYS cc_start: 0.7844 (tttt) cc_final: 0.7550 (tttt) REVERT: B 637 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7068 (mm-30) REVERT: B 648 SER cc_start: 0.8634 (p) cc_final: 0.8368 (m) REVERT: B 680 ASP cc_start: 0.7499 (m-30) cc_final: 0.7105 (m-30) outliers start: 12 outliers final: 10 residues processed: 216 average time/residue: 0.4667 time to fit residues: 137.3136 Evaluate side-chains 223 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 212 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 70 optimal weight: 0.0670 chunk 106 optimal weight: 0.9990 chunk 98 optimal weight: 0.0970 chunk 84 optimal weight: 0.3980 chunk 8 optimal weight: 0.3980 chunk 65 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9085 Z= 0.151 Angle : 0.443 4.842 12354 Z= 0.241 Chirality : 0.033 0.144 1409 Planarity : 0.003 0.048 1508 Dihedral : 3.694 19.097 1166 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.15 % Allowed : 11.26 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 2.75 (0.26), residues: 1053 helix: 2.06 (0.17), residues: 830 sheet: None (None), residues: 0 loop : 1.13 (0.50), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 PHE 0.018 0.001 PHE A 499 TYR 0.014 0.001 TYR A 256 ARG 0.004 0.000 ARG A 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2106 Ramachandran restraints generated. 1053 Oldfield, 0 Emsley, 1053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 209 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6563 (mt-10) REVERT: A 150 SER cc_start: 0.8013 (OUTLIER) cc_final: 0.7712 (m) REVERT: A 166 ASP cc_start: 0.7177 (t0) cc_final: 0.6602 (m-30) REVERT: A 186 ILE cc_start: 0.8166 (tp) cc_final: 0.7895 (mt) REVERT: A 322 MET cc_start: 0.7180 (tpp) cc_final: 0.6902 (tpp) REVERT: A 326 MET cc_start: 0.7580 (ttm) cc_final: 0.7307 (ttm) REVERT: A 537 ARG cc_start: 0.7349 (ttm170) cc_final: 0.7043 (ttm170) REVERT: A 547 ASN cc_start: 0.8312 (t0) cc_final: 0.8097 (t0) REVERT: A 607 ASP cc_start: 0.8320 (t0) cc_final: 0.8069 (t0) REVERT: A 678 GLU cc_start: 0.7932 (tp30) cc_final: 0.7677 (tm-30) REVERT: B 136 PHE cc_start: 0.7813 (m-10) cc_final: 0.7536 (m-10) REVERT: B 166 ASP cc_start: 0.8002 (t0) cc_final: 0.7757 (m-30) REVERT: B 309 LYS cc_start: 0.7897 (tttt) cc_final: 0.7612 (mtpp) REVERT: B 321 GLN cc_start: 0.7288 (mt0) cc_final: 0.6917 (mt0) REVERT: B 329 LYS cc_start: 0.8633 (tptt) cc_final: 0.8325 (tptt) REVERT: B 637 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.7021 (mm-30) REVERT: B 648 SER cc_start: 0.8653 (p) cc_final: 0.8399 (m) REVERT: B 680 ASP cc_start: 0.7479 (m-30) cc_final: 0.7104 (m-30) outliers start: 11 outliers final: 8 residues processed: 214 average time/residue: 0.4745 time to fit residues: 138.9387 Evaluate side-chains 219 residues out of total 959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 209 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 637 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 87 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.0870 chunk 74 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.169264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.140071 restraints weight = 38992.165| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.26 r_work: 0.3708 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9085 Z= 0.188 Angle : 0.454 6.447 12354 Z= 0.247 Chirality : 0.034 0.143 1409 Planarity : 0.003 0.044 1508 Dihedral : 3.662 19.025 1166 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.04 % Allowed : 11.37 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 2.79 (0.26), residues: 1053 helix: 2.10 (0.17), residues: 830 sheet: None (None), residues: 0 loop : 1.08 (0.50), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 223 HIS 0.002 0.001 HIS B 134 PHE 0.018 0.001 PHE A 499 TYR 0.015 0.001 TYR A 256 ARG 0.003 0.000 ARG A 424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5142.13 seconds wall clock time: 91 minutes 24.37 seconds (5484.37 seconds total)