Starting phenix.real_space_refine on Wed Mar 4 05:27:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c8d_30305/03_2026/7c8d_30305.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c8d_30305/03_2026/7c8d_30305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7c8d_30305/03_2026/7c8d_30305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c8d_30305/03_2026/7c8d_30305.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c8d_30305/03_2026/7c8d_30305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c8d_30305/03_2026/7c8d_30305.map" } resolution = 3.0 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6104 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 4074 2.51 5 N 1058 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6359 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4815 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 568} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ASP:plan': 1, 'TRP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.20, per 1000 atoms: 0.19 Number of scatterers: 6359 At special positions: 0 Unit cell: (96.3937, 93.4125, 107.325, 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) Zn 1 29.99 S 36 16.00 O 1190 8.00 N 1058 7.00 C 4074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.05 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 148.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 801 " - pdb=" NE2 HIS A 374 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 7 sheets defined 53.3% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.692A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 removed outlier: 3.551A pdb=" N LYS A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 removed outlier: 4.278A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 128 removed outlier: 3.575A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.665A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 252 removed outlier: 3.512A pdb=" N LYS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 4.212A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.704A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.577A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.750A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.605A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.549A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.814A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.503A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 4.435A pdb=" N LYS A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.843A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.512A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.212A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.112A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.784A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474 290 hydrogen bonds defined for protein. 822 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: 0.91 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2037 1.35 - 1.48: 1777 1.48 - 1.61: 2669 1.61 - 1.73: 0 1.73 - 1.86: 56 Bond restraints: 6539 Sorted by residual: bond pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 1.808 1.862 -0.054 3.30e-02 9.18e+02 2.71e+00 bond pdb=" N VAL A 364 " pdb=" CA VAL A 364 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.23e-02 6.61e+03 9.96e-01 bond pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta sigma weight residual 1.458 1.445 0.013 1.48e-02 4.57e+03 7.81e-01 bond pdb=" CA ASP B 364 " pdb=" C ASP B 364 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.08e-02 8.57e+03 7.57e-01 bond pdb=" CA TYR A 83 " pdb=" CB TYR A 83 " ideal model delta sigma weight residual 1.528 1.542 -0.014 1.68e-02 3.54e+03 6.57e-01 ... (remaining 6534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 8727 1.56 - 3.12: 134 3.12 - 4.68: 18 4.68 - 6.24: 9 6.24 - 7.80: 1 Bond angle restraints: 8889 Sorted by residual: angle pdb=" C PRO A 135 " pdb=" N ASN A 136 " pdb=" CA ASN A 136 " ideal model delta sigma weight residual 121.54 126.34 -4.80 1.91e+00 2.74e-01 6.31e+00 angle pdb=" N ASP A 499 " pdb=" CA ASP A 499 " pdb=" C ASP A 499 " ideal model delta sigma weight residual 109.81 114.93 -5.12 2.21e+00 2.05e-01 5.36e+00 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 119.57 -5.17 2.30e+00 1.89e-01 5.06e+00 angle pdb=" CA LEU B 335 " pdb=" CB LEU B 335 " pdb=" CG LEU B 335 " ideal model delta sigma weight residual 116.30 124.10 -7.80 3.50e+00 8.16e-02 4.97e+00 angle pdb=" N CYS B 432 " pdb=" CA CYS B 432 " pdb=" C CYS B 432 " ideal model delta sigma weight residual 108.60 111.76 -3.16 1.46e+00 4.69e-01 4.69e+00 ... (remaining 8884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3364 17.84 - 35.68: 356 35.68 - 53.52: 102 53.52 - 71.36: 20 71.36 - 89.20: 21 Dihedral angle restraints: 3863 sinusoidal: 1540 harmonic: 2323 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual -86.00 -33.10 -52.90 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual -86.00 -37.81 -48.19 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" CA THR B 500 " pdb=" C THR B 500 " pdb=" N ASN B 501 " pdb=" CA ASN B 501 " ideal model delta harmonic sigma weight residual 180.00 157.46 22.54 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 3860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 551 0.031 - 0.061: 280 0.061 - 0.092: 65 0.092 - 0.122: 38 0.122 - 0.153: 2 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA VAL A 283 " pdb=" N VAL A 283 " pdb=" C VAL A 283 " pdb=" CB VAL A 283 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ASN B 501 " pdb=" N ASN B 501 " pdb=" C ASN B 501 " pdb=" CB ASN B 501 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 933 not shown) Planarity restraints: 1146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO B 384 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO A 235 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 489 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO A 490 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 490 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 490 " 0.016 5.00e-02 4.00e+02 ... (remaining 1143 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 68 2.58 - 3.16: 5111 3.16 - 3.74: 10330 3.74 - 4.32: 14653 4.32 - 4.90: 23826 Nonbonded interactions: 53988 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 801 " model vdw 1.998 2.230 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.158 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.188 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.196 3.120 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.217 3.040 ... (remaining 53983 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.220 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 0.202 6548 Z= 0.182 Angle : 0.537 7.804 8903 Z= 0.303 Chirality : 0.040 0.153 936 Planarity : 0.004 0.036 1146 Dihedral : 17.372 89.203 2352 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 6.05 % Allowed : 20.21 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -2.80 (0.26), residues: 788 helix: -1.60 (0.23), residues: 390 sheet: -0.38 (0.88), residues: 36 loop : -2.25 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.010 0.001 TYR A 385 PHE 0.010 0.001 PHE A 308 TRP 0.014 0.001 TRP A 163 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6539) covalent geometry : angle 0.53112 ( 8889) SS BOND : bond 0.00827 ( 7) SS BOND : angle 2.03517 ( 14) hydrogen bonds : bond 0.17411 ( 290) hydrogen bonds : angle 6.87241 ( 822) metal coordination : bond 0.20170 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.250 Fit side-chains REVERT: A 62 MET cc_start: 0.7469 (ttt) cc_final: 0.7189 (ttp) REVERT: A 363 LYS cc_start: 0.6862 (mmtp) cc_final: 0.6278 (mttp) REVERT: A 510 TYR cc_start: 0.8058 (m-80) cc_final: 0.7856 (m-80) REVERT: A 579 MET cc_start: 0.8197 (ttm) cc_final: 0.7966 (ttm) outliers start: 41 outliers final: 11 residues processed: 160 average time/residue: 0.5081 time to fit residues: 85.5620 Evaluate side-chains 106 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.0050 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 290 ASN A 322 ASN A 345 HIS A 416 ASN A 598 GLN B 354 ASN B 360 ASN B 506 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.158709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131519 restraints weight = 8801.674| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.04 r_work: 0.3461 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 6548 Z= 0.217 Angle : 0.632 15.651 8903 Z= 0.332 Chirality : 0.045 0.218 936 Planarity : 0.005 0.064 1146 Dihedral : 6.261 58.925 876 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.16 % Allowed : 23.16 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.75 (0.28), residues: 788 helix: -0.62 (0.25), residues: 394 sheet: -0.35 (0.92), residues: 36 loop : -1.83 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 115 TYR 0.014 0.002 TYR A 385 PHE 0.011 0.002 PHE A 308 TRP 0.013 0.002 TRP A 168 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00505 ( 6539) covalent geometry : angle 0.62819 ( 8889) SS BOND : bond 0.00890 ( 7) SS BOND : angle 1.96154 ( 14) hydrogen bonds : bond 0.05035 ( 290) hydrogen bonds : angle 4.99679 ( 822) metal coordination : bond 0.00608 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.152 Fit side-chains REVERT: A 62 MET cc_start: 0.7818 (ttt) cc_final: 0.7471 (ttp) REVERT: A 79 LEU cc_start: 0.8897 (mt) cc_final: 0.8520 (mp) REVERT: A 287 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6641 (pp30) REVERT: A 312 GLU cc_start: 0.7476 (tt0) cc_final: 0.7242 (tt0) REVERT: A 363 LYS cc_start: 0.6886 (mmtp) cc_final: 0.6319 (mttp) REVERT: A 503 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8540 (tt) REVERT: A 603 PHE cc_start: 0.6634 (t80) cc_final: 0.6241 (t80) REVERT: B 403 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7361 (ptm160) REVERT: B 515 PHE cc_start: 0.6367 (m-80) cc_final: 0.5856 (m-80) outliers start: 35 outliers final: 17 residues processed: 133 average time/residue: 0.4153 time to fit residues: 58.8519 Evaluate side-chains 108 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 403 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS B 501 ASN B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.159785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132486 restraints weight = 8718.978| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.01 r_work: 0.3480 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6548 Z= 0.125 Angle : 0.543 14.047 8903 Z= 0.279 Chirality : 0.041 0.168 936 Planarity : 0.004 0.034 1146 Dihedral : 5.561 58.987 868 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.57 % Allowed : 23.89 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.04 (0.29), residues: 788 helix: 0.02 (0.27), residues: 393 sheet: -0.09 (0.96), residues: 36 loop : -1.53 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 306 TYR 0.012 0.001 TYR B 351 PHE 0.010 0.001 PHE A 315 TRP 0.015 0.001 TRP A 163 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6539) covalent geometry : angle 0.53900 ( 8889) SS BOND : bond 0.00830 ( 7) SS BOND : angle 1.73763 ( 14) hydrogen bonds : bond 0.04042 ( 290) hydrogen bonds : angle 4.66277 ( 822) metal coordination : bond 0.00167 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7783 (ttt) cc_final: 0.7459 (ttp) REVERT: A 157 ASP cc_start: 0.7791 (t70) cc_final: 0.7414 (t0) REVERT: A 160 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6935 (tm-30) REVERT: A 287 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6547 (pp30) REVERT: A 306 ARG cc_start: 0.6951 (tpt-90) cc_final: 0.6480 (ttt180) REVERT: A 312 GLU cc_start: 0.7411 (tt0) cc_final: 0.7197 (tt0) REVERT: A 363 LYS cc_start: 0.6891 (mmtp) cc_final: 0.6309 (mttp) REVERT: A 478 TRP cc_start: 0.7994 (m100) cc_final: 0.7707 (m100) REVERT: A 503 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8462 (tt) REVERT: A 603 PHE cc_start: 0.6476 (t80) cc_final: 0.6151 (t80) REVERT: B 493 GLN cc_start: 0.5925 (tm-30) cc_final: 0.5681 (tm130) REVERT: B 515 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.5667 (m-80) outliers start: 31 outliers final: 13 residues processed: 133 average time/residue: 0.4828 time to fit residues: 67.9156 Evaluate side-chains 121 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 62 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 598 GLN B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126182 restraints weight = 8842.666| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.00 r_work: 0.3401 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 6548 Z= 0.378 Angle : 0.771 14.571 8903 Z= 0.404 Chirality : 0.051 0.229 936 Planarity : 0.006 0.082 1146 Dihedral : 6.414 58.112 867 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 8.26 % Allowed : 21.09 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.46 (0.29), residues: 788 helix: -0.46 (0.25), residues: 385 sheet: -0.66 (0.85), residues: 46 loop : -1.50 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 115 TYR 0.018 0.003 TYR A 613 PHE 0.017 0.003 PHE A 308 TRP 0.014 0.003 TRP A 271 HIS 0.007 0.002 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00890 ( 6539) covalent geometry : angle 0.76731 ( 8889) SS BOND : bond 0.01165 ( 7) SS BOND : angle 2.11088 ( 14) hydrogen bonds : bond 0.05969 ( 290) hydrogen bonds : angle 5.18117 ( 822) metal coordination : bond 0.00469 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 91 time to evaluate : 0.250 Fit side-chains REVERT: A 79 LEU cc_start: 0.8922 (mt) cc_final: 0.8559 (mp) REVERT: A 208 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8141 (tp30) REVERT: A 249 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7412 (mtm) REVERT: A 254 SER cc_start: 0.7324 (p) cc_final: 0.7061 (p) REVERT: A 306 ARG cc_start: 0.7007 (tpt-90) cc_final: 0.6572 (ttt180) REVERT: B 405 ASP cc_start: 0.8591 (p0) cc_final: 0.8372 (p0) REVERT: B 486 PHE cc_start: 0.5865 (OUTLIER) cc_final: 0.5582 (t80) REVERT: B 501 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7586 (t0) outliers start: 56 outliers final: 28 residues processed: 136 average time/residue: 0.4097 time to fit residues: 59.3471 Evaluate side-chains 120 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 481 ASN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 290 ASN A 598 GLN B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.160737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.133530 restraints weight = 8744.993| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.06 r_work: 0.3496 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6548 Z= 0.122 Angle : 0.560 14.081 8903 Z= 0.287 Chirality : 0.041 0.166 936 Planarity : 0.004 0.035 1146 Dihedral : 5.694 56.795 867 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.46 % Allowed : 23.89 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.84 (0.30), residues: 788 helix: 0.16 (0.27), residues: 394 sheet: 0.04 (0.99), residues: 36 loop : -1.42 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 340 TYR 0.010 0.001 TYR B 453 PHE 0.011 0.001 PHE A 315 TRP 0.016 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6539) covalent geometry : angle 0.55468 ( 8889) SS BOND : bond 0.00905 ( 7) SS BOND : angle 2.05629 ( 14) hydrogen bonds : bond 0.04037 ( 290) hydrogen bonds : angle 4.70227 ( 822) metal coordination : bond 0.00113 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.253 Fit side-chains REVERT: A 157 ASP cc_start: 0.7833 (t70) cc_final: 0.7452 (t0) REVERT: A 160 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6936 (tm-30) REVERT: A 254 SER cc_start: 0.7303 (p) cc_final: 0.7007 (p) REVERT: A 411 SER cc_start: 0.8210 (OUTLIER) cc_final: 0.8007 (m) REVERT: A 478 TRP cc_start: 0.8040 (m100) cc_final: 0.7760 (m100) REVERT: A 516 TYR cc_start: 0.8544 (t80) cc_final: 0.7761 (t80) REVERT: A 603 PHE cc_start: 0.6597 (t80) cc_final: 0.6291 (t80) REVERT: B 355 ARG cc_start: 0.7457 (ttm170) cc_final: 0.7162 (ttm170) REVERT: B 493 GLN cc_start: 0.5984 (tm-30) cc_final: 0.5760 (tm130) REVERT: B 501 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7430 (t0) REVERT: B 516 GLU cc_start: 0.5500 (OUTLIER) cc_final: 0.4447 (pp20) outliers start: 37 outliers final: 13 residues processed: 132 average time/residue: 0.4522 time to fit residues: 63.2931 Evaluate side-chains 113 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS A 598 GLN B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.156927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129524 restraints weight = 8813.961| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.99 r_work: 0.3437 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6548 Z= 0.177 Angle : 0.652 18.260 8903 Z= 0.333 Chirality : 0.044 0.219 936 Planarity : 0.004 0.046 1146 Dihedral : 5.910 57.088 867 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 5.46 % Allowed : 24.34 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.75 (0.30), residues: 788 helix: 0.20 (0.26), residues: 392 sheet: -0.47 (0.81), residues: 48 loop : -1.26 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 531 TYR 0.021 0.002 TYR B 449 PHE 0.014 0.002 PHE A 308 TRP 0.013 0.002 TRP A 163 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 6539) covalent geometry : angle 0.64009 ( 8889) SS BOND : bond 0.00894 ( 7) SS BOND : angle 3.25316 ( 14) hydrogen bonds : bond 0.04510 ( 290) hydrogen bonds : angle 4.80412 ( 822) metal coordination : bond 0.00188 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 92 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 157 ASP cc_start: 0.7909 (t70) cc_final: 0.7562 (t0) REVERT: A 208 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8033 (tp30) REVERT: A 249 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7290 (mtm) REVERT: A 254 SER cc_start: 0.7331 (p) cc_final: 0.7049 (p) REVERT: A 306 ARG cc_start: 0.6959 (tpt-90) cc_final: 0.6527 (ttt180) REVERT: A 478 TRP cc_start: 0.8042 (m100) cc_final: 0.7718 (m100) REVERT: B 501 ASN cc_start: 0.7937 (OUTLIER) cc_final: 0.7507 (t0) REVERT: B 516 GLU cc_start: 0.5760 (OUTLIER) cc_final: 0.4817 (pp20) outliers start: 37 outliers final: 19 residues processed: 122 average time/residue: 0.4265 time to fit residues: 55.4123 Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 9 optimal weight: 0.0070 chunk 72 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS B 493 GLN B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.161532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.134252 restraints weight = 8733.547| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.02 r_work: 0.3497 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6548 Z= 0.110 Angle : 0.579 17.433 8903 Z= 0.293 Chirality : 0.041 0.167 936 Planarity : 0.004 0.035 1146 Dihedral : 5.526 56.961 867 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.69 % Allowed : 26.40 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.37 (0.30), residues: 788 helix: 0.61 (0.27), residues: 391 sheet: 0.01 (0.94), residues: 38 loop : -1.21 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 531 TYR 0.016 0.001 TYR B 449 PHE 0.011 0.001 PHE B 429 TRP 0.017 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 6539) covalent geometry : angle 0.56708 ( 8889) SS BOND : bond 0.00678 ( 7) SS BOND : angle 3.03358 ( 14) hydrogen bonds : bond 0.03734 ( 290) hydrogen bonds : angle 4.66987 ( 822) metal coordination : bond 0.00059 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ASP cc_start: 0.7818 (t70) cc_final: 0.7551 (t0) REVERT: A 465 LYS cc_start: 0.8182 (mttt) cc_final: 0.7703 (mtpt) REVERT: A 478 TRP cc_start: 0.7980 (m100) cc_final: 0.7711 (m100) REVERT: A 516 TYR cc_start: 0.8563 (t80) cc_final: 0.7935 (t80) REVERT: B 501 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7407 (t0) REVERT: B 515 PHE cc_start: 0.5995 (OUTLIER) cc_final: 0.3109 (m-80) REVERT: B 516 GLU cc_start: 0.5647 (OUTLIER) cc_final: 0.4603 (pp20) outliers start: 25 outliers final: 12 residues processed: 114 average time/residue: 0.4624 time to fit residues: 55.8467 Evaluate side-chains 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS A 598 GLN B 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.161034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.133459 restraints weight = 8763.662| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.04 r_work: 0.3488 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6548 Z= 0.121 Angle : 0.590 17.442 8903 Z= 0.300 Chirality : 0.041 0.172 936 Planarity : 0.004 0.058 1146 Dihedral : 5.349 57.385 867 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.83 % Allowed : 26.40 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.23 (0.31), residues: 788 helix: 0.72 (0.27), residues: 390 sheet: -0.63 (0.80), residues: 48 loop : -1.04 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 454 TYR 0.016 0.001 TYR B 396 PHE 0.016 0.001 PHE A 308 TRP 0.016 0.001 TRP A 302 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6539) covalent geometry : angle 0.57628 ( 8889) SS BOND : bond 0.00628 ( 7) SS BOND : angle 3.23085 ( 14) hydrogen bonds : bond 0.03873 ( 290) hydrogen bonds : angle 4.61170 ( 822) metal coordination : bond 0.00097 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7650 (ttt) cc_final: 0.7444 (ttp) REVERT: A 465 LYS cc_start: 0.8166 (mttt) cc_final: 0.7650 (mtpt) REVERT: A 478 TRP cc_start: 0.7960 (m100) cc_final: 0.7587 (m100) REVERT: A 516 TYR cc_start: 0.8583 (t80) cc_final: 0.7791 (t80) REVERT: B 501 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7433 (t0) outliers start: 26 outliers final: 14 residues processed: 111 average time/residue: 0.4122 time to fit residues: 48.8795 Evaluate side-chains 100 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 ASN A 345 HIS ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.161651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134024 restraints weight = 8853.408| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.05 r_work: 0.3510 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6548 Z= 0.120 Angle : 0.681 25.832 8903 Z= 0.342 Chirality : 0.042 0.260 936 Planarity : 0.004 0.052 1146 Dihedral : 5.223 57.540 867 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.54 % Allowed : 26.70 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.11 (0.31), residues: 788 helix: 0.77 (0.27), residues: 391 sheet: -0.37 (0.82), residues: 46 loop : -0.96 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 454 TYR 0.019 0.001 TYR A 183 PHE 0.020 0.001 PHE A 308 TRP 0.016 0.001 TRP A 302 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6539) covalent geometry : angle 0.65234 ( 8889) SS BOND : bond 0.01095 ( 7) SS BOND : angle 4.93584 ( 14) hydrogen bonds : bond 0.03927 ( 290) hydrogen bonds : angle 4.57017 ( 822) metal coordination : bond 0.00077 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7644 (ttt) cc_final: 0.7443 (ttp) REVERT: A 465 LYS cc_start: 0.8132 (mttt) cc_final: 0.7636 (mtpt) REVERT: A 478 TRP cc_start: 0.7949 (m100) cc_final: 0.7624 (m100) REVERT: A 503 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8421 (tt) REVERT: A 516 TYR cc_start: 0.8578 (t80) cc_final: 0.7841 (t80) REVERT: B 501 ASN cc_start: 0.7719 (OUTLIER) cc_final: 0.7363 (t0) REVERT: B 515 PHE cc_start: 0.5913 (OUTLIER) cc_final: 0.2976 (m-80) outliers start: 24 outliers final: 14 residues processed: 107 average time/residue: 0.4333 time to fit residues: 49.2318 Evaluate side-chains 105 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.161105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.133660 restraints weight = 8645.328| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.03 r_work: 0.3504 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6548 Z= 0.129 Angle : 0.714 27.115 8903 Z= 0.357 Chirality : 0.043 0.302 936 Planarity : 0.004 0.053 1146 Dihedral : 5.263 57.402 867 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.24 % Allowed : 27.43 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.04 (0.31), residues: 788 helix: 0.80 (0.27), residues: 391 sheet: -0.19 (0.82), residues: 46 loop : -0.91 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 454 TYR 0.018 0.002 TYR A 183 PHE 0.022 0.001 PHE A 308 TRP 0.023 0.002 TRP A 302 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6539) covalent geometry : angle 0.68586 ( 8889) SS BOND : bond 0.01123 ( 7) SS BOND : angle 5.09181 ( 14) hydrogen bonds : bond 0.04007 ( 290) hydrogen bonds : angle 4.47530 ( 822) metal coordination : bond 0.00123 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 62 MET cc_start: 0.7651 (ttt) cc_final: 0.7447 (ttp) REVERT: A 287 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6743 (mm-40) REVERT: A 465 LYS cc_start: 0.8141 (mttt) cc_final: 0.7638 (mtpt) REVERT: A 478 TRP cc_start: 0.7940 (m100) cc_final: 0.7595 (m100) REVERT: A 503 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8445 (tt) REVERT: A 516 TYR cc_start: 0.8593 (t80) cc_final: 0.7747 (t80) REVERT: B 355 ARG cc_start: 0.7436 (ttm170) cc_final: 0.7200 (ttm170) REVERT: B 501 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7472 (t0) REVERT: B 515 PHE cc_start: 0.5918 (OUTLIER) cc_final: 0.2910 (m-80) outliers start: 22 outliers final: 14 residues processed: 111 average time/residue: 0.4659 time to fit residues: 54.8877 Evaluate side-chains 104 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 516 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 0.2980 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 345 HIS ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.162888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136042 restraints weight = 8828.594| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.99 r_work: 0.3519 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6548 Z= 0.123 Angle : 0.682 26.731 8903 Z= 0.344 Chirality : 0.043 0.336 936 Planarity : 0.004 0.050 1146 Dihedral : 5.131 57.308 867 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.54 % Allowed : 27.58 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.05 (0.31), residues: 788 helix: 0.89 (0.28), residues: 391 sheet: 0.59 (0.96), residues: 36 loop : -0.96 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 454 TYR 0.017 0.001 TYR A 183 PHE 0.017 0.001 PHE A 308 TRP 0.021 0.001 TRP A 302 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 6539) covalent geometry : angle 0.65464 ( 8889) SS BOND : bond 0.00977 ( 7) SS BOND : angle 4.90188 ( 14) hydrogen bonds : bond 0.03897 ( 290) hydrogen bonds : angle 4.33170 ( 822) metal coordination : bond 0.00096 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2370.04 seconds wall clock time: 41 minutes 0.84 seconds (2460.84 seconds total)