Starting phenix.real_space_refine on Thu Jul 2 13:55:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l76_62870/07_2026/9l76_62870.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l76_62870/07_2026/9l76_62870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l76_62870/07_2026/9l76_62870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l76_62870/07_2026/9l76_62870.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l76_62870/07_2026/9l76_62870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l76_62870/07_2026/9l76_62870.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 P 7 5.49 5 S 56 5.16 5 C 5583 2.51 5 N 1412 2.21 5 O 1546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8604 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "C" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3423 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 445} Chain: "D" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "A" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3423 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 445} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'PC1': 1, 'PKZ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PKZ:plan-1': 1, 'PKZ:plan-3': 1, 'PKZ:plan-5': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PKZ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PKZ:plan-1': 1, 'PKZ:plan-3': 1, 'PKZ:plan-5': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 1.67, per 1000 atoms: 0.19 Number of scatterers: 8604 At special positions: 0 Unit cell: (69.7, 95.94, 97.58, 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 56 16.00 P 7 15.00 O 1546 8.00 N 1412 7.00 C 5583 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 320.9 milliseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 2 sheets defined 75.3% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'B' and resid 405 through 418 removed outlier: 3.701A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 443 Processing helix chain 'B' and resid 444 through 445 No H-bonds generated for 'chain 'B' and resid 444 through 445' Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 449 through 461 Processing helix chain 'B' and resid 464 through 473 removed outlier: 3.865A pdb=" N ALA B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 508 removed outlier: 3.688A pdb=" N ARG B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 23 Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 29 through 50 Processing helix chain 'C' and resid 56 through 78 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 82 through 108 Processing helix chain 'C' and resid 114 through 148 Processing helix chain 'C' and resid 159 through 181 Processing helix chain 'C' and resid 183 through 208 Processing helix chain 'C' and resid 210 through 212 No H-bonds generated for 'chain 'C' and resid 210 through 212' Processing helix chain 'C' and resid 213 through 236 Processing helix chain 'C' and resid 238 through 264 Processing helix chain 'C' and resid 266 through 272 Processing helix chain 'C' and resid 273 through 278 removed outlier: 4.172A pdb=" N THR C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP C 278 " --> pdb=" O GLY C 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 273 through 278' Processing helix chain 'C' and resid 295 through 306 Processing helix chain 'C' and resid 314 through 320 removed outlier: 3.881A pdb=" N ALA C 318 " --> pdb=" O GLY C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 336 Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.795A pdb=" N VAL C 357 " --> pdb=" O GLY C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.610A pdb=" N ASP C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 391 through 399 removed outlier: 3.606A pdb=" N VAL C 394 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Proline residue: C 396 - end of helix Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 436 through 441 removed outlier: 3.643A pdb=" N PHE C 440 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 462 Processing helix chain 'D' and resid 407 through 418 Processing helix chain 'D' and resid 421 through 443 Processing helix chain 'D' and resid 444 through 445 No H-bonds generated for 'chain 'D' and resid 444 through 445' Processing helix chain 'D' and resid 446 through 448 No H-bonds generated for 'chain 'D' and resid 446 through 448' Processing helix chain 'D' and resid 449 through 462 Processing helix chain 'D' and resid 464 through 472 removed outlier: 3.947A pdb=" N ALA D 468 " --> pdb=" O ILE D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 475 No H-bonds generated for 'chain 'D' and resid 473 through 475' Processing helix chain 'D' and resid 476 through 508 removed outlier: 3.674A pdb=" N ARG D 508 " --> pdb=" O LEU D 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 24 Processing helix chain 'A' and resid 26 through 50 removed outlier: 4.503A pdb=" N ARG A 31 " --> pdb=" O HIS A 27 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLN A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 78 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 108 Processing helix chain 'A' and resid 114 through 148 Processing helix chain 'A' and resid 159 through 181 Processing helix chain 'A' and resid 183 through 208 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 213 through 237 Processing helix chain 'A' and resid 238 through 264 Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 295 through 306 Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.481A pdb=" N ASP A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 450 through 462 Processing sheet with id=AA1, first strand: chain 'C' and resid 369 through 371 removed outlier: 8.461A pdb=" N LEU C 370 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N PHE C 342 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL C 309 " --> pdb=" O ARG C 341 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLY C 343 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE C 311 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL C 420 " --> pdb=" O HIS C 445 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU C 447 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL C 422 " --> pdb=" O LEU C 447 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 369 through 371 removed outlier: 8.316A pdb=" N LEU A 370 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N PHE A 342 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL A 385 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL A 420 " --> pdb=" O HIS A 445 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1863 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: 1.48 Time building geometry restraints manager: 1.10 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: 1372 1.31 - 1.44: 2255 1.44 - 1.56: 5030 1.56 - 1.69: 16 1.69 - 1.82: 108 Bond restraints: 8781 Sorted by residual: bond pdb=" C2B PKZ A 501 " pdb=" C3B PKZ A 501 " ideal model delta sigma weight residual 1.529 1.331 0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C2B PKZ C 502 " pdb=" C3B PKZ C 502 " ideal model delta sigma weight residual 1.529 1.333 0.196 2.00e-02 2.50e+03 9.65e+01 bond pdb=" C1B PKZ C 502 " pdb=" O4B PKZ C 502 " ideal model delta sigma weight residual 1.390 1.570 -0.180 2.00e-02 2.50e+03 8.13e+01 bond pdb=" C1B PKZ A 501 " pdb=" O4B PKZ A 501 " ideal model delta sigma weight residual 1.390 1.569 -0.179 2.00e-02 2.50e+03 8.04e+01 bond pdb=" C4B PKZ A 501 " pdb=" O4B PKZ A 501 " ideal model delta sigma weight residual 1.437 1.312 0.125 2.00e-02 2.50e+03 3.94e+01 ... (remaining 8776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 11798 3.02 - 6.04: 112 6.04 - 9.06: 20 9.06 - 12.07: 11 12.07 - 15.09: 7 Bond angle restraints: 11948 Sorted by residual: angle pdb=" C TYR C 431 " pdb=" CA TYR C 431 " pdb=" CB TYR C 431 " ideal model delta sigma weight residual 116.54 110.58 5.96 1.15e+00 7.56e-01 2.69e+01 angle pdb=" O3A PKZ C 502 " pdb=" P1A PKZ C 502 " pdb=" O5B PKZ C 502 " ideal model delta sigma weight residual 94.17 109.26 -15.09 3.00e+00 1.11e-01 2.53e+01 angle pdb=" O3A PKZ A 501 " pdb=" P1A PKZ A 501 " pdb=" O5B PKZ A 501 " ideal model delta sigma weight residual 94.17 108.71 -14.54 3.00e+00 1.11e-01 2.35e+01 angle pdb=" O12 PC1 C 501 " pdb=" P PC1 C 501 " pdb=" O14 PC1 C 501 " ideal model delta sigma weight residual 123.67 109.19 14.48 3.00e+00 1.11e-01 2.33e+01 angle pdb=" O1A PKZ A 501 " pdb=" P1A PKZ A 501 " pdb=" O2A PKZ A 501 " ideal model delta sigma weight residual 122.06 109.54 12.52 3.00e+00 1.11e-01 1.74e+01 ... (remaining 11943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4357 17.98 - 35.97: 555 35.97 - 53.95: 150 53.95 - 71.93: 24 71.93 - 89.91: 6 Dihedral angle restraints: 5092 sinusoidal: 1878 harmonic: 3214 Sorted by residual: dihedral pdb=" CA VAL C 434 " pdb=" C VAL C 434 " pdb=" N GLN C 435 " pdb=" CA GLN C 435 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA MET C 409 " pdb=" C MET C 409 " pdb=" N PRO C 410 " pdb=" CA PRO C 410 " ideal model delta harmonic sigma weight residual 180.00 163.46 16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ALA A 318 " pdb=" C ALA A 318 " pdb=" N VAL A 319 " pdb=" CA VAL A 319 " ideal model delta harmonic sigma weight residual 180.00 164.54 15.46 0 5.00e+00 4.00e-02 9.56e+00 ... (remaining 5089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1082 0.046 - 0.091: 277 0.091 - 0.136: 60 0.136 - 0.182: 7 0.182 - 0.227: 1 Chirality restraints: 1427 Sorted by residual: chirality pdb=" C3B PKZ C 502 " pdb=" C2B PKZ C 502 " pdb=" C4B PKZ C 502 " pdb=" O3B PKZ C 502 " both_signs ideal model delta sigma weight residual False -2.66 -2.43 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE B 411 " pdb=" CA ILE B 411 " pdb=" CG1 ILE B 411 " pdb=" CG2 ILE B 411 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" C3B PKZ A 501 " pdb=" C2B PKZ A 501 " pdb=" C4B PKZ A 501 " pdb=" O3B PKZ A 501 " both_signs ideal model delta sigma weight residual False -2.66 -2.49 -0.17 2.00e-01 2.50e+01 7.39e-01 ... (remaining 1424 not shown) Planarity restraints: 1480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 214 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.60e+00 pdb=" N PRO A 215 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 415 " 0.009 2.00e-02 2.50e+03 1.16e-02 3.35e+00 pdb=" CG TRP B 415 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 415 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 415 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 415 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 415 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 415 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 415 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 415 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 415 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 345 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 346 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 346 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 346 " -0.023 5.00e-02 4.00e+02 ... (remaining 1477 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 541 2.73 - 3.27: 9379 3.27 - 3.81: 15972 3.81 - 4.36: 17830 4.36 - 4.90: 31099 Nonbonded interactions: 74821 Sorted by model distance: nonbonded pdb=" N GLU A 374 " pdb=" OE1 GLU A 374 " model vdw 2.187 3.120 nonbonded pdb=" O VAL A 288 " pdb=" ND1 HIS A 291 " model vdw 2.264 3.120 nonbonded pdb=" O LEU C 100 " pdb=" ND2 ASN C 104 " model vdw 2.268 3.120 nonbonded pdb=" OG SER C 266 " pdb=" OG SER C 269 " model vdw 2.276 3.040 nonbonded pdb=" OG SER A 281 " pdb=" OD2 ASP A 284 " model vdw 2.287 3.040 ... (remaining 74816 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 462) selection = (chain 'C' and resid 1 through 462) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 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: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.750 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 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 : 0.007 0.198 8781 Z= 0.335 Angle : 0.803 15.093 11948 Z= 0.353 Chirality : 0.041 0.227 1427 Planarity : 0.004 0.047 1480 Dihedral : 17.291 89.912 3036 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.53 % Favored : 96.29 % Rotamer: Outliers : 3.59 % Allowed : 33.52 % Favored : 62.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.26), residues: 1132 helix: 2.47 (0.18), residues: 782 sheet: -0.85 (0.67), residues: 60 loop : -0.53 (0.41), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 350 TYR 0.013 0.001 TYR D 440 PHE 0.009 0.001 PHE B 480 TRP 0.031 0.001 TRP B 415 HIS 0.006 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.33 ( 8781) covalent geometry : angle 0.80273 / 0.35 (11948) hydrogen bonds : bond 0.09862 / 6.15 ( 637) hydrogen bonds : angle 4.52627 / 3.37 ( 1863) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.301 Fit side-chains outliers start: 32 outliers final: 27 residues processed: 159 average time/residue: 0.3627 time to fit residues: 62.8227 Evaluate side-chains 155 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 431 TYR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 GLN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 HIS A 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.102517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.073747 restraints weight = 14416.639| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.74 r_work: 0.2869 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8781 Z= 0.153 Angle : 0.536 6.648 11948 Z= 0.274 Chirality : 0.040 0.161 1427 Planarity : 0.004 0.046 1480 Dihedral : 7.197 53.300 1265 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.53 % Favored : 96.29 % Rotamer: Outliers : 4.15 % Allowed : 27.24 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.26), residues: 1132 helix: 2.52 (0.18), residues: 788 sheet: -0.95 (0.65), residues: 68 loop : -0.39 (0.43), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 292 TYR 0.011 0.001 TYR C 106 PHE 0.010 0.001 PHE B 424 TRP 0.015 0.001 TRP B 415 HIS 0.004 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 8781) covalent geometry : angle 0.53599 / 0.27 (11948) hydrogen bonds : bond 0.03638 / 2.35 ( 637) hydrogen bonds : angle 3.87675 / 2.88 ( 1863) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.248 Fit side-chains REVERT: B 412 LEU cc_start: 0.9136 (mm) cc_final: 0.8859 (mm) REVERT: C 418 GLN cc_start: 0.8692 (tt0) cc_final: 0.8182 (tm-30) outliers start: 37 outliers final: 10 residues processed: 157 average time/residue: 0.3854 time to fit residues: 65.7650 Evaluate side-chains 133 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 94 optimal weight: 0.4980 chunk 111 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 222 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 = 0.3497 r_free = 0.3497 target = 0.103649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.074774 restraints weight = 14273.926| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.76 r_work: 0.2897 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8781 Z= 0.122 Angle : 0.522 7.593 11948 Z= 0.263 Chirality : 0.039 0.151 1427 Planarity : 0.004 0.044 1480 Dihedral : 5.711 50.909 1231 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.53 % Favored : 96.20 % Rotamer: Outliers : 3.92 % Allowed : 26.68 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.26), residues: 1132 helix: 2.60 (0.18), residues: 788 sheet: -0.96 (0.65), residues: 68 loop : -0.39 (0.43), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 292 TYR 0.017 0.001 TYR B 439 PHE 0.009 0.001 PHE B 480 TRP 0.010 0.001 TRP B 415 HIS 0.002 0.000 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 8781) covalent geometry : angle 0.52177 / 0.26 (11948) hydrogen bonds : bond 0.03372 / 2.17 ( 637) hydrogen bonds : angle 3.74825 / 2.78 ( 1863) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.334 Fit side-chains REVERT: B 412 LEU cc_start: 0.9191 (mm) cc_final: 0.8902 (mm) REVERT: B 415 TRP cc_start: 0.8088 (t-100) cc_final: 0.7824 (t-100) REVERT: C 418 GLN cc_start: 0.8671 (tt0) cc_final: 0.8251 (tm-30) REVERT: D 408 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7979 (tm) REVERT: D 507 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7512 (t80) REVERT: A 374 GLU cc_start: 0.8336 (mp0) cc_final: 0.8121 (mp0) REVERT: A 440 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7652 (t80) outliers start: 35 outliers final: 10 residues processed: 152 average time/residue: 0.3694 time to fit residues: 61.0924 Evaluate side-chains 141 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 440 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 108 HIS ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.102279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.073139 restraints weight = 14300.048| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.84 r_work: 0.2866 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8781 Z= 0.138 Angle : 0.522 7.527 11948 Z= 0.264 Chirality : 0.040 0.137 1427 Planarity : 0.004 0.038 1480 Dihedral : 5.586 60.820 1225 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.98 % Favored : 95.76 % Rotamer: Outliers : 4.37 % Allowed : 26.68 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.26), residues: 1132 helix: 2.60 (0.18), residues: 788 sheet: -0.98 (0.65), residues: 68 loop : -0.31 (0.43), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 292 TYR 0.011 0.001 TYR A 106 PHE 0.008 0.001 PHE B 424 TRP 0.007 0.001 TRP B 415 HIS 0.004 0.001 HIS C 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 8781) covalent geometry : angle 0.52220 / 0.26 (11948) hydrogen bonds : bond 0.03386 / 2.18 ( 637) hydrogen bonds : angle 3.72585 / 2.77 ( 1863) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.193 Fit side-chains REVERT: B 412 LEU cc_start: 0.9199 (mm) cc_final: 0.8899 (mm) REVERT: B 415 TRP cc_start: 0.8065 (t-100) cc_final: 0.7858 (t-100) REVERT: C 381 ASP cc_start: 0.8570 (t0) cc_final: 0.8279 (t0) REVERT: C 418 GLN cc_start: 0.8676 (tt0) cc_final: 0.8263 (tm-30) REVERT: D 408 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7991 (tm) REVERT: D 505 LYS cc_start: 0.8142 (ttmm) cc_final: 0.7827 (ttmm) REVERT: A 440 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7603 (t80) outliers start: 39 outliers final: 14 residues processed: 154 average time/residue: 0.3458 time to fit residues: 58.2259 Evaluate side-chains 138 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 0.0000 chunk 56 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 222 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 = 0.3472 r_free = 0.3472 target = 0.101038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.071779 restraints weight = 14327.944| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.83 r_work: 0.2813 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8781 Z= 0.168 Angle : 0.540 7.854 11948 Z= 0.273 Chirality : 0.040 0.138 1427 Planarity : 0.004 0.039 1480 Dihedral : 5.302 50.990 1223 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.80 % Favored : 95.94 % Rotamer: Outliers : 4.48 % Allowed : 25.90 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.26), residues: 1132 helix: 2.53 (0.18), residues: 786 sheet: -0.98 (0.64), residues: 68 loop : -0.30 (0.43), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 292 TYR 0.013 0.001 TYR B 439 PHE 0.010 0.001 PHE A 178 TRP 0.006 0.001 TRP B 415 HIS 0.002 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 8781) covalent geometry : angle 0.53972 / 0.27 (11948) hydrogen bonds : bond 0.03532 / 2.28 ( 637) hydrogen bonds : angle 3.79772 / 2.82 ( 1863) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 0.286 Fit side-chains REVERT: B 412 LEU cc_start: 0.9203 (mm) cc_final: 0.8899 (mm) REVERT: B 415 TRP cc_start: 0.8077 (t-100) cc_final: 0.7848 (t-100) REVERT: C 418 GLN cc_start: 0.8657 (tt0) cc_final: 0.8248 (tm-30) REVERT: D 408 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8003 (tm) REVERT: D 507 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.7437 (t80) REVERT: A 61 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8529 (mm) outliers start: 40 outliers final: 14 residues processed: 155 average time/residue: 0.3792 time to fit residues: 63.4789 Evaluate side-chains 140 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 222 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 = 0.3489 r_free = 0.3489 target = 0.102104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.073078 restraints weight = 14236.887| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.84 r_work: 0.2834 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8781 Z= 0.143 Angle : 0.548 8.547 11948 Z= 0.275 Chirality : 0.040 0.143 1427 Planarity : 0.004 0.038 1480 Dihedral : 5.249 51.717 1223 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.15 % Favored : 95.58 % Rotamer: Outliers : 2.69 % Allowed : 28.03 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.26), residues: 1132 helix: 2.54 (0.18), residues: 788 sheet: -1.03 (0.65), residues: 68 loop : -0.34 (0.43), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 292 TYR 0.013 0.001 TYR A 106 PHE 0.008 0.001 PHE A 178 TRP 0.007 0.001 TRP B 415 HIS 0.002 0.000 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8781) covalent geometry : angle 0.54805 / 0.27 (11948) hydrogen bonds : bond 0.03413 / 2.20 ( 637) hydrogen bonds : angle 3.77766 / 2.81 ( 1863) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.234 Fit side-chains REVERT: B 412 LEU cc_start: 0.9208 (mm) cc_final: 0.8906 (mm) REVERT: B 415 TRP cc_start: 0.8113 (t-100) cc_final: 0.7872 (t-100) REVERT: C 418 GLN cc_start: 0.8625 (tt0) cc_final: 0.8220 (tm-30) REVERT: D 408 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8007 (tm) REVERT: D 505 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7818 (ttmm) REVERT: D 507 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7494 (t80) REVERT: A 61 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8526 (mm) outliers start: 24 outliers final: 14 residues processed: 140 average time/residue: 0.4215 time to fit residues: 63.5788 Evaluate side-chains 138 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 0.0470 chunk 8 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 222 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 = 0.3499 r_free = 0.3499 target = 0.102931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.074189 restraints weight = 14389.219| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.84 r_work: 0.2840 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8781 Z= 0.134 Angle : 0.542 9.038 11948 Z= 0.273 Chirality : 0.040 0.147 1427 Planarity : 0.004 0.038 1480 Dihedral : 5.220 52.078 1223 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.71 % Favored : 96.02 % Rotamer: Outliers : 3.36 % Allowed : 27.69 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.26), residues: 1132 helix: 2.55 (0.18), residues: 788 sheet: -1.04 (0.65), residues: 68 loop : -0.36 (0.42), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 292 TYR 0.017 0.001 TYR B 439 PHE 0.007 0.001 PHE B 424 TRP 0.009 0.001 TRP D 415 HIS 0.002 0.000 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 8781) covalent geometry : angle 0.54178 / 0.27 (11948) hydrogen bonds : bond 0.03376 / 2.17 ( 637) hydrogen bonds : angle 3.75947 / 2.79 ( 1863) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.227 Fit side-chains REVERT: B 412 LEU cc_start: 0.9224 (mm) cc_final: 0.8920 (mm) REVERT: C 418 GLN cc_start: 0.8610 (tt0) cc_final: 0.8207 (tm-30) REVERT: D 408 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8007 (tm) REVERT: D 444 ASN cc_start: 0.9151 (t0) cc_final: 0.8880 (t160) REVERT: D 507 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7377 (t80) REVERT: A 61 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8511 (mm) REVERT: A 261 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8600 (ttmm) outliers start: 30 outliers final: 15 residues processed: 146 average time/residue: 0.3544 time to fit residues: 56.1854 Evaluate side-chains 142 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.101282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.072449 restraints weight = 14280.283| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.81 r_work: 0.2851 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8781 Z= 0.162 Angle : 0.553 9.574 11948 Z= 0.280 Chirality : 0.041 0.154 1427 Planarity : 0.004 0.038 1480 Dihedral : 5.235 53.004 1223 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.89 % Favored : 95.85 % Rotamer: Outliers : 3.03 % Allowed : 28.36 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.26), residues: 1132 helix: 2.48 (0.18), residues: 788 sheet: -1.04 (0.65), residues: 68 loop : -0.31 (0.43), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 292 TYR 0.015 0.001 TYR A 106 PHE 0.008 0.001 PHE B 424 TRP 0.029 0.001 TRP B 415 HIS 0.002 0.000 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 ( 8781) covalent geometry : angle 0.55324 / 0.28 (11948) hydrogen bonds : bond 0.03506 / 2.26 ( 637) hydrogen bonds : angle 3.81549 / 2.83 ( 1863) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.209 Fit side-chains REVERT: B 412 LEU cc_start: 0.9216 (mm) cc_final: 0.8907 (mm) REVERT: C 409 MET cc_start: 0.9329 (ttp) cc_final: 0.9114 (ttm) REVERT: C 418 GLN cc_start: 0.8615 (tt0) cc_final: 0.8221 (tm-30) REVERT: D 408 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8023 (tm) REVERT: D 505 LYS cc_start: 0.8148 (ttmm) cc_final: 0.7844 (ttmm) REVERT: D 507 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7493 (t80) REVERT: A 61 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8514 (mm) REVERT: A 261 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8583 (ttmm) outliers start: 27 outliers final: 14 residues processed: 142 average time/residue: 0.3760 time to fit residues: 57.8272 Evaluate side-chains 139 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 222 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 = 0.3476 r_free = 0.3476 target = 0.101420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.072527 restraints weight = 14235.294| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.80 r_work: 0.2816 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8781 Z= 0.162 Angle : 0.576 10.148 11948 Z= 0.287 Chirality : 0.041 0.158 1427 Planarity : 0.004 0.038 1480 Dihedral : 5.249 54.295 1223 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.80 % Favored : 95.94 % Rotamer: Outliers : 2.58 % Allowed : 28.92 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.26), residues: 1132 helix: 2.48 (0.18), residues: 786 sheet: -1.06 (0.65), residues: 68 loop : -0.34 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 292 TYR 0.021 0.002 TYR B 439 PHE 0.009 0.001 PHE B 424 TRP 0.025 0.001 TRP B 415 HIS 0.002 0.000 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 8781) covalent geometry : angle 0.57606 / 0.29 (11948) hydrogen bonds : bond 0.03503 / 2.26 ( 637) hydrogen bonds : angle 3.83272 / 2.84 ( 1863) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.238 Fit side-chains REVERT: B 412 LEU cc_start: 0.9222 (mm) cc_final: 0.8905 (mm) REVERT: C 409 MET cc_start: 0.9363 (ttp) cc_final: 0.9092 (ttm) REVERT: C 418 GLN cc_start: 0.8616 (tt0) cc_final: 0.8225 (tm-30) REVERT: D 408 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8021 (tm) REVERT: D 507 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7439 (t80) REVERT: A 61 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8504 (mm) REVERT: A 261 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8613 (ttmm) outliers start: 23 outliers final: 13 residues processed: 139 average time/residue: 0.3920 time to fit residues: 58.6631 Evaluate side-chains 137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 95 optimal weight: 0.0770 chunk 84 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 0.0060 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 ASN C 187 GLN ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.104465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.076015 restraints weight = 14386.074| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.84 r_work: 0.2886 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8781 Z= 0.121 Angle : 0.565 10.043 11948 Z= 0.281 Chirality : 0.040 0.157 1427 Planarity : 0.004 0.038 1480 Dihedral : 5.150 57.874 1223 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.06 % Favored : 95.67 % Rotamer: Outliers : 1.91 % Allowed : 29.37 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.26), residues: 1132 helix: 2.57 (0.18), residues: 786 sheet: -0.99 (0.67), residues: 68 loop : -0.40 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 350 TYR 0.014 0.001 TYR A 106 PHE 0.008 0.001 PHE B 483 TRP 0.027 0.001 TRP B 415 HIS 0.013 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 8781) covalent geometry : angle 0.56546 / 0.28 (11948) hydrogen bonds : bond 0.03274 / 2.09 ( 637) hydrogen bonds : angle 3.75621 / 2.78 ( 1863) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.279 Fit side-chains REVERT: B 412 LEU cc_start: 0.9226 (mm) cc_final: 0.8930 (mm) REVERT: C 418 GLN cc_start: 0.8600 (tt0) cc_final: 0.8219 (tm-30) REVERT: D 408 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8013 (tm) REVERT: D 444 ASN cc_start: 0.9162 (t0) cc_final: 0.8955 (t160) REVERT: D 471 GLN cc_start: 0.8917 (mt0) cc_final: 0.8269 (pt0) REVERT: D 507 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7421 (t80) REVERT: A 61 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8465 (mm) outliers start: 17 outliers final: 8 residues processed: 143 average time/residue: 0.3663 time to fit residues: 57.0664 Evaluate side-chains 137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 0.3980 chunk 94 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.103203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.074544 restraints weight = 14318.122| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.83 r_work: 0.2857 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8781 Z= 0.141 Angle : 0.572 10.096 11948 Z= 0.284 Chirality : 0.041 0.163 1427 Planarity : 0.004 0.038 1480 Dihedral : 5.143 57.319 1223 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.71 % Favored : 96.02 % Rotamer: Outliers : 1.68 % Allowed : 29.82 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.26), residues: 1132 helix: 2.52 (0.18), residues: 788 sheet: -1.03 (0.66), residues: 68 loop : -0.35 (0.42), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 292 TYR 0.015 0.001 TYR A 106 PHE 0.012 0.001 PHE B 480 TRP 0.024 0.001 TRP B 415 HIS 0.013 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 8781) covalent geometry : angle 0.57190 / 0.28 (11948) hydrogen bonds : bond 0.03336 / 2.13 ( 637) hydrogen bonds : angle 3.77864 / 2.80 ( 1863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2059.22 seconds wall clock time: 35 minutes 57.58 seconds (2157.58 seconds total)