Starting phenix.real_space_refine on Mon Mar 11 04:40:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b4l_12002/03_2024/7b4l_12002_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b4l_12002/03_2024/7b4l_12002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b4l_12002/03_2024/7b4l_12002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b4l_12002/03_2024/7b4l_12002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b4l_12002/03_2024/7b4l_12002_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b4l_12002/03_2024/7b4l_12002_updated.pdb" } resolution = 3.1 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= 0.100 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 36 5.16 5 Na 2 4.78 5 C 4740 2.51 5 N 1068 2.21 5 O 1180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 515": "NH1" <-> "NH2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 384": "OE1" <-> "OE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B ARG 515": "NH1" <-> "NH2" Residue "B GLU 521": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7030 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3300 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 423} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3300 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 423} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 202 Unusual residues: {' NA': 1, 'C14': 3, 'POV': 2, 'UND': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 202 Unusual residues: {' NA': 1, 'C14': 3, 'POV': 2, 'UND': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="NA NA A 601 " occ=0.50 residue: pdb="NA NA B 602 " occ=0.50 residue: pdb=" O HOH A 711 " occ=0.50 residue: pdb=" O HOH B 711 " occ=0.50 Time building chain proxies: 4.44, per 1000 atoms: 0.63 Number of scatterers: 7030 At special positions: 0 Unit cell: (97.643, 91.205, 77.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 4 15.00 Na 2 11.00 O 1180 8.00 N 1068 7.00 C 4740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.70 Conformation dependent library (CDL) restraints added in 1.3 seconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 0 sheets defined 75.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 83 through 105 removed outlier: 3.510A pdb=" N ILE A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 114 through 133 Processing helix chain 'A' and resid 145 through 158 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 170 through 189 Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.517A pdb=" N LYS A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 223 Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 231 through 240 removed outlier: 3.523A pdb=" N ILE A 236 " --> pdb=" O GLN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 Proline residue: A 251 - end of helix removed outlier: 3.764A pdb=" N LEU A 255 " --> pdb=" O PRO A 251 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 273 Processing helix chain 'A' and resid 277 through 294 removed outlier: 3.585A pdb=" N ILE A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 327 removed outlier: 3.626A pdb=" N GLY A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 307 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.639A pdb=" N GLY A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 407 removed outlier: 3.641A pdb=" N ILE A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) Proline residue: A 398 - end of helix Processing helix chain 'A' and resid 419 through 439 removed outlier: 3.570A pdb=" N VAL A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 462 through 467 Processing helix chain 'A' and resid 470 through 478 Processing helix chain 'A' and resid 482 through 516 removed outlier: 3.683A pdb=" N ASP A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Proline residue: A 503 - end of helix Proline residue: A 514 - end of helix Processing helix chain 'B' and resid 83 through 105 removed outlier: 3.510A pdb=" N ILE B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 114 through 133 Processing helix chain 'B' and resid 145 through 158 Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 170 through 189 Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.517A pdb=" N LYS B 199 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 223 Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 231 through 240 removed outlier: 3.523A pdb=" N ILE B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 259 Proline residue: B 251 - end of helix removed outlier: 3.764A pdb=" N LEU B 255 " --> pdb=" O PRO B 251 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 273 Processing helix chain 'B' and resid 277 through 294 removed outlier: 3.585A pdb=" N ILE B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 327 removed outlier: 3.626A pdb=" N GLY B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 307 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 327 " --> pdb=" O PHE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 Processing helix chain 'B' and resid 362 through 377 removed outlier: 3.639A pdb=" N GLY B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 407 removed outlier: 3.641A pdb=" N ILE B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) Proline residue: B 398 - end of helix Processing helix chain 'B' and resid 419 through 439 removed outlier: 3.570A pdb=" N VAL B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 455 Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'B' and resid 470 through 478 Processing helix chain 'B' and resid 482 through 516 removed outlier: 3.683A pdb=" N ASP B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) Proline residue: B 503 - end of helix Proline residue: B 514 - end of helix 438 hydrogen bonds defined for protein. 1314 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: 1.85 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1016 1.31 - 1.43: 1700 1.43 - 1.56: 4346 1.56 - 1.69: 8 1.69 - 1.81: 52 Bond restraints: 7122 Sorted by residual: bond pdb=" C31 POV A 602 " pdb=" O31 POV A 602 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C31 POV B 603 " pdb=" O31 POV B 603 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C31 POV B 601 " pdb=" O31 POV B 601 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C31 POV A 611 " pdb=" O31 POV A 611 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C21 POV B 603 " pdb=" O21 POV B 603 " ideal model delta sigma weight residual 1.330 1.400 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 7117 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.18: 201 107.18 - 113.90: 4394 113.90 - 120.61: 2829 120.61 - 127.33: 2076 127.33 - 134.05: 72 Bond angle restraints: 9572 Sorted by residual: angle pdb=" O11 POV B 601 " pdb=" P POV B 601 " pdb=" O12 POV B 601 " ideal model delta sigma weight residual 97.67 109.84 -12.17 3.00e+00 1.11e-01 1.65e+01 angle pdb=" O11 POV A 611 " pdb=" P POV A 611 " pdb=" O12 POV A 611 " ideal model delta sigma weight residual 97.67 109.82 -12.15 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O13 POV B 601 " pdb=" P POV B 601 " pdb=" O14 POV B 601 " ideal model delta sigma weight residual 121.11 109.21 11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O13 POV A 611 " pdb=" P POV A 611 " pdb=" O14 POV A 611 " ideal model delta sigma weight residual 121.11 109.21 11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O13 POV A 602 " pdb=" P POV A 602 " pdb=" O14 POV A 602 " ideal model delta sigma weight residual 121.11 109.62 11.49 3.00e+00 1.11e-01 1.47e+01 ... (remaining 9567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.04: 3824 20.04 - 40.08: 326 40.08 - 60.13: 86 60.13 - 80.17: 10 80.17 - 100.21: 2 Dihedral angle restraints: 4248 sinusoidal: 1778 harmonic: 2470 Sorted by residual: dihedral pdb=" CA TYR B 326 " pdb=" C TYR B 326 " pdb=" N PHE B 327 " pdb=" CA PHE B 327 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TYR A 326 " pdb=" C TYR A 326 " pdb=" N PHE A 327 " pdb=" CA PHE A 327 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA PHE A 327 " pdb=" C PHE A 327 " pdb=" N PRO A 328 " pdb=" CA PRO A 328 " ideal model delta harmonic sigma weight residual 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 4245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 787 0.037 - 0.075: 307 0.075 - 0.112: 38 0.112 - 0.149: 10 0.149 - 0.187: 4 Chirality restraints: 1146 Sorted by residual: chirality pdb=" CB THR B 417 " pdb=" CA THR B 417 " pdb=" OG1 THR B 417 " pdb=" CG2 THR B 417 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CB THR A 417 " pdb=" CA THR A 417 " pdb=" OG1 THR A 417 " pdb=" CG2 THR A 417 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CG LEU B 483 " pdb=" CB LEU B 483 " pdb=" CD1 LEU B 483 " pdb=" CD2 LEU B 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.36e-01 ... (remaining 1143 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 110 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.45e+00 pdb=" N PRO A 111 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 111 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 111 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 110 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO B 111 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 111 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 111 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 502 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO A 503 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " -0.022 5.00e-02 4.00e+02 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 120 2.69 - 3.24: 7010 3.24 - 3.80: 10348 3.80 - 4.35: 14521 4.35 - 4.90: 24249 Nonbonded interactions: 56248 Sorted by model distance: nonbonded pdb=" O SER B 497 " pdb=" OG1 THR B 501 " model vdw 2.141 2.440 nonbonded pdb=" O SER A 497 " pdb=" OG1 THR A 501 " model vdw 2.141 2.440 nonbonded pdb=" O PHE B 445 " pdb=" NZ LYS B 450 " model vdw 2.282 2.520 nonbonded pdb=" O PHE A 445 " pdb=" NZ LYS A 450 " model vdw 2.283 2.520 nonbonded pdb=" O LYS B 450 " pdb=" OG SER B 454 " model vdw 2.297 2.440 ... (remaining 56243 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 79 through 521 or resid 604 through 605 or resid 607 throu \ gh 610)) selection = (chain 'B' and (resid 79 through 521 or resid 604 through 605 or resid 607 throu \ gh 610)) } 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=0.50 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.180 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.370 Find NCS groups from input model: 0.420 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 : 0.005 0.072 7122 Z= 0.309 Angle : 1.048 12.169 9572 Z= 0.442 Chirality : 0.039 0.187 1146 Planarity : 0.005 0.053 1122 Dihedral : 16.182 100.208 2672 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.27), residues: 882 helix: -0.07 (0.19), residues: 696 sheet: None (None), residues: 0 loop : -2.28 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 378 HIS 0.001 0.000 HIS A 224 PHE 0.009 0.001 PHE B 401 TYR 0.007 0.001 TYR B 123 ARG 0.006 0.001 ARG B 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.762 Fit side-chains REVERT: A 149 MET cc_start: 0.8974 (mtt) cc_final: 0.8530 (mtm) REVERT: A 198 LYS cc_start: 0.8365 (ttpt) cc_final: 0.7817 (mmtt) REVERT: A 489 ASP cc_start: 0.7389 (m-30) cc_final: 0.7153 (m-30) REVERT: B 149 MET cc_start: 0.8975 (mtt) cc_final: 0.8530 (mtm) REVERT: B 198 LYS cc_start: 0.8367 (ttpt) cc_final: 0.7824 (mmtt) REVERT: B 489 ASP cc_start: 0.7391 (m-30) cc_final: 0.7153 (m-30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1853 time to fit residues: 29.6009 Evaluate side-chains 88 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7122 Z= 0.193 Angle : 0.602 9.107 9572 Z= 0.301 Chirality : 0.040 0.151 1146 Planarity : 0.005 0.058 1122 Dihedral : 14.732 99.833 1236 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.68 % Allowed : 7.84 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.28), residues: 882 helix: 0.84 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -2.06 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 98 HIS 0.001 0.000 HIS B 224 PHE 0.013 0.001 PHE A 154 TYR 0.005 0.001 TYR B 123 ARG 0.002 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.767 Fit side-chains REVERT: A 198 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7616 (mmtt) REVERT: A 253 MET cc_start: 0.8903 (mmm) cc_final: 0.8514 (mmm) REVERT: A 407 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: B 198 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7622 (mmtt) REVERT: B 253 MET cc_start: 0.8879 (mmm) cc_final: 0.8475 (mmm) REVERT: B 407 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6804 (mp0) outliers start: 12 outliers final: 4 residues processed: 100 average time/residue: 0.1498 time to fit residues: 21.6493 Evaluate side-chains 96 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 417 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN B 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7122 Z= 0.184 Angle : 0.549 8.534 9572 Z= 0.274 Chirality : 0.040 0.125 1146 Planarity : 0.004 0.056 1122 Dihedral : 14.030 84.597 1236 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.36 % Allowed : 9.80 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.28), residues: 882 helix: 1.05 (0.20), residues: 698 sheet: None (None), residues: 0 loop : -2.08 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 98 HIS 0.001 0.000 HIS B 224 PHE 0.014 0.001 PHE A 323 TYR 0.004 0.001 TYR B 123 ARG 0.002 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.682 Fit side-chains REVERT: A 85 ASP cc_start: 0.7181 (OUTLIER) cc_final: 0.6682 (t70) REVERT: A 198 LYS cc_start: 0.8398 (ttpt) cc_final: 0.7690 (mmtt) REVERT: A 253 MET cc_start: 0.8869 (mmm) cc_final: 0.8564 (mmm) REVERT: A 489 ASP cc_start: 0.7735 (m-30) cc_final: 0.7493 (t70) REVERT: B 85 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6685 (t70) REVERT: B 198 LYS cc_start: 0.8396 (ttpt) cc_final: 0.7696 (mmtt) REVERT: B 253 MET cc_start: 0.8840 (mmm) cc_final: 0.8521 (mmm) REVERT: B 489 ASP cc_start: 0.7735 (m-30) cc_final: 0.7495 (t70) outliers start: 24 outliers final: 16 residues processed: 100 average time/residue: 0.1585 time to fit residues: 22.4402 Evaluate side-chains 104 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 482 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7122 Z= 0.234 Angle : 0.579 8.999 9572 Z= 0.286 Chirality : 0.041 0.145 1146 Planarity : 0.005 0.062 1122 Dihedral : 13.630 62.900 1236 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.20 % Allowed : 11.48 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.28), residues: 882 helix: 1.02 (0.19), residues: 702 sheet: None (None), residues: 0 loop : -1.93 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 98 HIS 0.002 0.001 HIS B 224 PHE 0.012 0.001 PHE A 401 TYR 0.008 0.001 TYR A 123 ARG 0.003 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 0.760 Fit side-chains REVERT: A 85 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6722 (t0) REVERT: A 198 LYS cc_start: 0.8409 (ttpt) cc_final: 0.7702 (mmtt) REVERT: A 324 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8405 (mt) REVERT: A 407 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6911 (mp0) REVERT: A 489 ASP cc_start: 0.7803 (m-30) cc_final: 0.7598 (m-30) REVERT: B 85 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6719 (t0) REVERT: B 198 LYS cc_start: 0.8412 (ttpt) cc_final: 0.7709 (mmtt) REVERT: B 324 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8406 (mt) REVERT: B 407 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: B 489 ASP cc_start: 0.7802 (m-30) cc_final: 0.7597 (m-30) outliers start: 30 outliers final: 18 residues processed: 112 average time/residue: 0.1966 time to fit residues: 30.1235 Evaluate side-chains 110 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 482 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.0000 chunk 72 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 0.0070 chunk 76 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS B 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7122 Z= 0.153 Angle : 0.542 8.488 9572 Z= 0.262 Chirality : 0.038 0.121 1146 Planarity : 0.004 0.054 1122 Dihedral : 12.897 61.167 1236 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.08 % Allowed : 12.61 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.29), residues: 882 helix: 1.35 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.88 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 98 HIS 0.001 0.000 HIS A 224 PHE 0.008 0.001 PHE B 401 TYR 0.007 0.001 TYR B 123 ARG 0.002 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 0.662 Fit side-chains REVERT: A 85 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6844 (t0) REVERT: A 198 LYS cc_start: 0.8412 (ttpt) cc_final: 0.7714 (mmtt) REVERT: A 253 MET cc_start: 0.8503 (mmm) cc_final: 0.7890 (mmm) REVERT: A 324 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8250 (mt) REVERT: B 85 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6842 (t0) REVERT: B 198 LYS cc_start: 0.8411 (ttpt) cc_final: 0.7718 (mmtt) REVERT: B 253 MET cc_start: 0.8481 (mmm) cc_final: 0.7866 (mmm) REVERT: B 324 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8253 (mt) outliers start: 22 outliers final: 12 residues processed: 110 average time/residue: 0.1938 time to fit residues: 29.0353 Evaluate side-chains 106 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 482 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS B 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7122 Z= 0.219 Angle : 0.561 8.243 9572 Z= 0.273 Chirality : 0.039 0.128 1146 Planarity : 0.005 0.062 1122 Dihedral : 12.798 60.356 1236 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.94 % Allowed : 13.59 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.29), residues: 882 helix: 1.26 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.87 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 98 HIS 0.002 0.001 HIS B 224 PHE 0.011 0.001 PHE B 495 TYR 0.008 0.001 TYR B 123 ARG 0.002 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.666 Fit side-chains REVERT: A 85 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.6993 (t0) REVERT: A 198 LYS cc_start: 0.8403 (ttpt) cc_final: 0.7753 (mmtt) REVERT: A 253 MET cc_start: 0.8653 (mmm) cc_final: 0.8175 (mmm) REVERT: A 324 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8379 (mt) REVERT: B 85 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6992 (t0) REVERT: B 198 LYS cc_start: 0.8401 (ttpt) cc_final: 0.7759 (mmtt) REVERT: B 253 MET cc_start: 0.8641 (mmm) cc_final: 0.8157 (mmm) REVERT: B 324 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8381 (mt) outliers start: 21 outliers final: 13 residues processed: 100 average time/residue: 0.1775 time to fit residues: 24.2819 Evaluate side-chains 101 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 482 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 62 optimal weight: 0.0470 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 0.0010 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS B 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7122 Z= 0.145 Angle : 0.506 6.902 9572 Z= 0.247 Chirality : 0.038 0.132 1146 Planarity : 0.004 0.053 1122 Dihedral : 12.255 59.995 1236 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.08 % Allowed : 13.87 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.29), residues: 882 helix: 1.52 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -1.68 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 98 HIS 0.001 0.000 HIS A 224 PHE 0.008 0.001 PHE A 495 TYR 0.009 0.001 TYR B 123 ARG 0.001 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.691 Fit side-chains REVERT: A 85 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6937 (t0) REVERT: A 198 LYS cc_start: 0.8262 (ttpt) cc_final: 0.7653 (mmtt) REVERT: A 253 MET cc_start: 0.8541 (mmm) cc_final: 0.8011 (mmm) REVERT: A 324 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8260 (mt) REVERT: A 489 ASP cc_start: 0.7765 (m-30) cc_final: 0.7523 (t0) REVERT: B 85 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6936 (t0) REVERT: B 198 LYS cc_start: 0.8260 (ttpt) cc_final: 0.7657 (mmtt) REVERT: B 253 MET cc_start: 0.8531 (mmm) cc_final: 0.7994 (mmm) REVERT: B 324 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8262 (mt) REVERT: B 489 ASP cc_start: 0.7767 (m-30) cc_final: 0.7528 (t0) outliers start: 22 outliers final: 14 residues processed: 114 average time/residue: 0.1711 time to fit residues: 26.7288 Evaluate side-chains 106 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 482 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS B 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7122 Z= 0.177 Angle : 0.531 7.836 9572 Z= 0.257 Chirality : 0.039 0.127 1146 Planarity : 0.004 0.061 1122 Dihedral : 12.143 59.853 1236 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.66 % Allowed : 15.83 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.29), residues: 882 helix: 1.45 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -1.69 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 98 HIS 0.001 0.000 HIS A 224 PHE 0.013 0.001 PHE A 495 TYR 0.008 0.001 TYR A 123 ARG 0.002 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 0.721 Fit side-chains REVERT: A 198 LYS cc_start: 0.8278 (ttpt) cc_final: 0.7715 (mmtt) REVERT: A 253 MET cc_start: 0.8588 (mmm) cc_final: 0.8151 (mmm) REVERT: A 324 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8350 (mt) REVERT: B 198 LYS cc_start: 0.8276 (ttpt) cc_final: 0.7718 (mmtt) REVERT: B 253 MET cc_start: 0.8600 (mmm) cc_final: 0.8047 (mmm) REVERT: B 324 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8353 (mt) outliers start: 19 outliers final: 15 residues processed: 100 average time/residue: 0.1636 time to fit residues: 23.2806 Evaluate side-chains 105 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 482 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN A 478 HIS B 325 GLN B 478 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7122 Z= 0.169 Angle : 0.524 7.393 9572 Z= 0.253 Chirality : 0.038 0.129 1146 Planarity : 0.004 0.045 1122 Dihedral : 11.981 59.892 1236 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.94 % Allowed : 15.27 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.29), residues: 882 helix: 1.46 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -1.56 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 98 HIS 0.001 0.000 HIS B 224 PHE 0.012 0.001 PHE A 495 TYR 0.007 0.001 TYR B 123 ARG 0.001 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 0.736 Fit side-chains REVERT: A 198 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7708 (mmtt) REVERT: A 253 MET cc_start: 0.8557 (mmm) cc_final: 0.8017 (mmm) REVERT: A 324 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8275 (mt) REVERT: B 198 LYS cc_start: 0.8269 (ttpt) cc_final: 0.7712 (mmtt) REVERT: B 253 MET cc_start: 0.8549 (mmm) cc_final: 0.7996 (mmm) REVERT: B 324 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8279 (mt) outliers start: 21 outliers final: 15 residues processed: 105 average time/residue: 0.1569 time to fit residues: 23.4230 Evaluate side-chains 103 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 482 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS B 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7122 Z= 0.197 Angle : 0.547 7.861 9572 Z= 0.265 Chirality : 0.039 0.125 1146 Planarity : 0.004 0.050 1122 Dihedral : 11.966 59.882 1236 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.38 % Allowed : 15.97 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.29), residues: 882 helix: 1.41 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -1.55 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 233 HIS 0.002 0.000 HIS A 224 PHE 0.013 0.001 PHE A 495 TYR 0.008 0.001 TYR A 123 ARG 0.001 0.000 ARG B 432 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.715 Fit side-chains REVERT: A 198 LYS cc_start: 0.8277 (ttpt) cc_final: 0.7714 (mmtt) REVERT: A 253 MET cc_start: 0.8565 (mmm) cc_final: 0.8144 (mmm) REVERT: A 324 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8300 (mt) REVERT: B 198 LYS cc_start: 0.8277 (ttpt) cc_final: 0.7721 (mmtt) REVERT: B 253 MET cc_start: 0.8558 (mmm) cc_final: 0.8127 (mmm) REVERT: B 324 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8302 (mt) outliers start: 17 outliers final: 14 residues processed: 97 average time/residue: 0.1632 time to fit residues: 22.3523 Evaluate side-chains 100 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 482 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.0870 chunk 3 optimal weight: 0.2980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 HIS B 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.163924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.147903 restraints weight = 8822.244| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.72 r_work: 0.3770 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7122 Z= 0.133 Angle : 0.510 6.830 9572 Z= 0.245 Chirality : 0.038 0.143 1146 Planarity : 0.004 0.044 1122 Dihedral : 11.463 59.737 1236 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.52 % Allowed : 15.83 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.29), residues: 882 helix: 1.62 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -1.55 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 98 HIS 0.001 0.000 HIS A 478 PHE 0.011 0.001 PHE B 495 TYR 0.007 0.001 TYR A 123 ARG 0.001 0.000 ARG B 414 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1594.92 seconds wall clock time: 29 minutes 51.73 seconds (1791.73 seconds total)