Starting phenix.real_space_refine on Thu Mar 13 01:19:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zkw_60210/03_2025/8zkw_60210.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zkw_60210/03_2025/8zkw_60210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zkw_60210/03_2025/8zkw_60210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zkw_60210/03_2025/8zkw_60210.map" model { file = "/net/cci-nas-00/data/ceres_data/8zkw_60210/03_2025/8zkw_60210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zkw_60210/03_2025/8zkw_60210.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 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 2 5.49 5 S 87 5.16 5 C 5649 2.51 5 N 1336 2.21 5 O 1430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8504 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4186 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 33, 'TRANS': 507} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4190 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 33, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.68, per 1000 atoms: 0.67 Number of scatterers: 8504 At special positions: 0 Unit cell: (86.7825, 99.18, 114.057, 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 87 16.00 P 2 15.00 O 1430 8.00 N 1336 7.00 C 5649 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 Links applied NAG-ASN " NAG A 602 " - " ASN A 261 " " NAG B 602 " - " ASN B 261 " Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.0 seconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 81.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 32 through 59 removed outlier: 6.781A pdb=" N LYS A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) Proline residue: A 50 - end of helix Proline residue: A 55 - end of helix Processing helix chain 'A' and resid 62 through 81 Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.982A pdb=" N VAL A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 103 through 111 Processing helix chain 'A' and resid 113 through 132 removed outlier: 3.820A pdb=" N CYS A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 Processing helix chain 'A' and resid 149 through 166 Processing helix chain 'A' and resid 169 through 191 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 220 through 238 Processing helix chain 'A' and resid 239 through 240 No H-bonds generated for 'chain 'A' and resid 239 through 240' Processing helix chain 'A' and resid 241 through 244 Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.622A pdb=" N LEU A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 295 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.659A pdb=" N GLN A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 removed outlier: 3.745A pdb=" N LEU A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 352 Processing helix chain 'A' and resid 360 through 365 removed outlier: 3.768A pdb=" N LEU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.582A pdb=" N THR A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 423 through 443 removed outlier: 4.189A pdb=" N PHE A 427 " --> pdb=" O TRP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 454 removed outlier: 4.147A pdb=" N GLY A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 458 Processing helix chain 'A' and resid 459 through 476 removed outlier: 3.558A pdb=" N ALA A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 499 Proline residue: A 489 - end of helix Processing helix chain 'A' and resid 501 through 513 removed outlier: 3.907A pdb=" N LEU A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 536 through 544 Processing helix chain 'A' and resid 544 through 567 removed outlier: 4.244A pdb=" N GLN A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'B' and resid 33 through 59 removed outlier: 6.561A pdb=" N LYS B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) Proline residue: B 50 - end of helix Proline residue: B 55 - end of helix Processing helix chain 'B' and resid 62 through 81 removed outlier: 3.747A pdb=" N ARG B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.914A pdb=" N VAL B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) Proline residue: B 97 - end of helix Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.587A pdb=" N TYR B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 149 through 166 Processing helix chain 'B' and resid 169 through 191 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 220 through 239 removed outlier: 3.842A pdb=" N CYS B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 259 removed outlier: 3.703A pdb=" N LEU B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 295 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 302 through 313 Processing helix chain 'B' and resid 315 through 327 Processing helix chain 'B' and resid 333 through 353 Processing helix chain 'B' and resid 372 through 386 removed outlier: 4.171A pdb=" N THR B 376 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 396 Processing helix chain 'B' and resid 413 through 421 Processing helix chain 'B' and resid 423 through 443 removed outlier: 4.220A pdb=" N PHE B 427 " --> pdb=" O TRP B 423 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 452 Processing helix chain 'B' and resid 453 through 458 removed outlier: 4.097A pdb=" N VAL B 457 " --> pdb=" O GLY B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 479 through 498 Proline residue: B 489 - end of helix Processing helix chain 'B' and resid 501 through 513 removed outlier: 3.854A pdb=" N LEU B 505 " --> pdb=" O HIS B 501 " (cutoff:3.500A) Proline residue: B 508 - end of helix Processing helix chain 'B' and resid 519 through 522 Processing helix chain 'B' and resid 523 through 534 Processing helix chain 'B' and resid 536 through 544 Processing helix chain 'B' and resid 544 through 567 removed outlier: 4.111A pdb=" N GLN B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY B 563 " --> pdb=" O CYS B 559 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 565 " --> pdb=" O THR B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 584 573 hydrogen bonds defined for protein. 1692 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: 2.60 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1298 1.32 - 1.44: 2294 1.44 - 1.57: 4985 1.57 - 1.69: 4 1.69 - 1.81: 145 Bond restraints: 8726 Sorted by residual: bond pdb=" N ILE A 448 " pdb=" CA ILE A 448 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.84e+00 bond pdb=" C PRO A 459 " pdb=" O PRO A 459 " ideal model delta sigma weight residual 1.233 1.200 0.033 1.18e-02 7.18e+03 7.66e+00 bond pdb=" N ILE A 453 " pdb=" CA ILE A 453 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.26e-02 6.30e+03 7.58e+00 bond pdb=" N VAL A 457 " pdb=" CA VAL A 457 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.26e-02 6.30e+03 7.54e+00 bond pdb=" N LEU A 458 " pdb=" CA LEU A 458 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.37e-02 5.33e+03 7.24e+00 ... (remaining 8721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 11565 1.87 - 3.74: 234 3.74 - 5.60: 54 5.60 - 7.47: 5 7.47 - 9.34: 3 Bond angle restraints: 11861 Sorted by residual: angle pdb=" CA TYR A 282 " pdb=" CB TYR A 282 " pdb=" CG TYR A 282 " ideal model delta sigma weight residual 113.90 121.26 -7.36 1.80e+00 3.09e-01 1.67e+01 angle pdb=" CA PRO A 459 " pdb=" C PRO A 459 " pdb=" O PRO A 459 " ideal model delta sigma weight residual 122.08 117.22 4.86 1.28e+00 6.10e-01 1.44e+01 angle pdb=" N GLU B 186 " pdb=" CA GLU B 186 " pdb=" CB GLU B 186 " ideal model delta sigma weight residual 110.12 115.70 -5.58 1.47e+00 4.63e-01 1.44e+01 angle pdb=" CA ASN A 460 " pdb=" C ASN A 460 " pdb=" O ASN A 460 " ideal model delta sigma weight residual 120.55 117.01 3.54 1.06e+00 8.90e-01 1.12e+01 angle pdb=" C TYR B 131 " pdb=" N CYS B 132 " pdb=" CA CYS B 132 " ideal model delta sigma weight residual 121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01 ... (remaining 11856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.99: 5014 24.99 - 49.97: 166 49.97 - 74.96: 15 74.96 - 99.94: 1 99.94 - 124.93: 3 Dihedral angle restraints: 5199 sinusoidal: 2069 harmonic: 3130 Sorted by residual: dihedral pdb=" CA ARG B 371 " pdb=" C ARG B 371 " pdb=" N ASN B 372 " pdb=" CA ASN B 372 " ideal model delta harmonic sigma weight residual 180.00 156.71 23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" C3 PTY A 601 " pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O12 PTY A 601 " ideal model delta sinusoidal sigma weight residual 300.23 175.30 124.93 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C3 PTY B 601 " pdb=" O11 PTY B 601 " pdb=" P1 PTY B 601 " pdb=" O12 PTY B 601 " ideal model delta sinusoidal sigma weight residual 300.23 178.07 122.16 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 5196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1279 0.080 - 0.160: 104 0.160 - 0.239: 4 0.239 - 0.319: 0 0.319 - 0.399: 1 Chirality restraints: 1388 Sorted by residual: chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 261 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CA LYS A 456 " pdb=" N LYS A 456 " pdb=" C LYS A 456 " pdb=" CB LYS A 456 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CA TYR B 282 " pdb=" N TYR B 282 " pdb=" C TYR B 282 " pdb=" CB TYR B 282 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 1385 not shown) Planarity restraints: 1445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 54 " 0.036 5.00e-02 4.00e+02 5.35e-02 4.59e+00 pdb=" N PRO A 55 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 55 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 55 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 559 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C CYS A 559 " 0.036 2.00e-02 2.50e+03 pdb=" O CYS A 559 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN A 560 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 523 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.12e+00 pdb=" N PRO A 524 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 524 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 524 " -0.024 5.00e-02 4.00e+02 ... (remaining 1442 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 74 2.66 - 3.22: 8698 3.22 - 3.78: 13596 3.78 - 4.34: 18169 4.34 - 4.90: 30364 Nonbonded interactions: 70901 Sorted by model distance: nonbonded pdb=" OD1 ASP B 114 " pdb=" OG SER B 373 " model vdw 2.101 3.040 nonbonded pdb=" OH TYR B 350 " pdb=" OG1 THR B 376 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR A 350 " pdb=" OG1 THR A 376 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASP A 316 " pdb=" N VAL A 317 " model vdw 2.324 3.120 nonbonded pdb=" OE1 GLN A 309 " pdb=" NH2 ARG A 312 " model vdw 2.335 3.120 ... (remaining 70896 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 32 through 147 or (resid 148 and (name N or name CA or nam \ e C or name O or name CB )) or resid 149 through 200 or (resid 213 and (name N o \ r name CA or name C or name O or name CB )) or resid 216 through 584 or resid 60 \ 1 through 602)) selection = (chain 'B' and (resid 32 through 298 or (resid 299 and (name N or name CA or nam \ e C or name O or name CB )) or resid 300 through 302 or (resid 303 through 305 a \ nd (name N or name CA or name C or name O or name CB )) or resid 306 through 397 \ or (resid 398 through 399 and (name N or name CA or name C or name O or name CB \ )) or resid 400 through 584 or resid 601 through 602)) } 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.710 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:29.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 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 0.051 8726 Z= 0.337 Angle : 0.685 9.339 11861 Z= 0.372 Chirality : 0.046 0.399 1388 Planarity : 0.005 0.054 1443 Dihedral : 12.728 124.929 3183 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1072 helix: 1.11 (0.18), residues: 799 sheet: None (None), residues: 0 loop : -0.99 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 414 HIS 0.014 0.002 HIS B 335 PHE 0.024 0.001 PHE B 251 TYR 0.028 0.002 TYR A 282 ARG 0.002 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.893 Fit side-chains REVERT: A 272 MET cc_start: 0.9447 (ttm) cc_final: 0.9232 (ttm) REVERT: A 363 ASP cc_start: 0.8780 (m-30) cc_final: 0.8539 (m-30) REVERT: A 369 ASP cc_start: 0.8146 (t0) cc_final: 0.7784 (OUTLIER) REVERT: B 349 MET cc_start: 0.9105 (mmm) cc_final: 0.8888 (mmm) outliers start: 0 outliers final: 2 residues processed: 89 average time/residue: 1.2159 time to fit residues: 115.6145 Evaluate side-chains 81 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.074622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.056740 restraints weight = 20092.071| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.83 r_work: 0.2664 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8726 Z= 0.228 Angle : 0.596 7.177 11861 Z= 0.305 Chirality : 0.042 0.338 1388 Planarity : 0.005 0.056 1443 Dihedral : 8.897 105.188 1273 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.33 % Allowed : 6.74 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.26), residues: 1072 helix: 1.35 (0.18), residues: 797 sheet: None (None), residues: 0 loop : -0.88 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 414 HIS 0.009 0.001 HIS B 335 PHE 0.025 0.001 PHE B 251 TYR 0.028 0.002 TYR B 282 ARG 0.003 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.842 Fit side-chains REVERT: A 295 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8172 (mtp) REVERT: A 363 ASP cc_start: 0.8839 (m-30) cc_final: 0.8592 (m-30) REVERT: B 316 ASP cc_start: 0.8986 (p0) cc_final: 0.8727 (t70) REVERT: B 349 MET cc_start: 0.8941 (mmm) cc_final: 0.8601 (mmm) outliers start: 12 outliers final: 3 residues processed: 88 average time/residue: 1.1799 time to fit residues: 111.5275 Evaluate side-chains 86 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain B residue 118 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.074481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.056483 restraints weight = 20498.939| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.86 r_work: 0.2659 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8726 Z= 0.249 Angle : 0.573 7.091 11861 Z= 0.292 Chirality : 0.041 0.325 1388 Planarity : 0.005 0.052 1443 Dihedral : 8.133 103.576 1271 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.88 % Allowed : 10.28 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.26), residues: 1072 helix: 1.41 (0.18), residues: 800 sheet: None (None), residues: 0 loop : -0.89 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 414 HIS 0.007 0.001 HIS B 335 PHE 0.026 0.001 PHE B 251 TYR 0.024 0.001 TYR B 282 ARG 0.001 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.957 Fit side-chains REVERT: A 295 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.7917 (mtp) REVERT: A 515 MET cc_start: 0.9021 (mpp) cc_final: 0.8798 (mpp) REVERT: B 316 ASP cc_start: 0.8991 (p0) cc_final: 0.8676 (t70) REVERT: B 349 MET cc_start: 0.8972 (mmm) cc_final: 0.8590 (mmm) outliers start: 8 outliers final: 3 residues processed: 91 average time/residue: 1.4036 time to fit residues: 137.0508 Evaluate side-chains 86 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain B residue 118 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 80 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 31 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.076486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.058776 restraints weight = 20315.592| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.86 r_work: 0.2710 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8726 Z= 0.156 Angle : 0.534 6.705 11861 Z= 0.272 Chirality : 0.040 0.315 1388 Planarity : 0.005 0.050 1443 Dihedral : 7.598 94.223 1271 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.44 % Allowed : 11.82 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1072 helix: 1.56 (0.18), residues: 797 sheet: None (None), residues: 0 loop : -0.89 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 414 HIS 0.005 0.001 HIS B 335 PHE 0.026 0.001 PHE B 251 TYR 0.024 0.001 TYR B 282 ARG 0.001 0.000 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.941 Fit side-chains REVERT: A 295 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.7462 (mtp) outliers start: 13 outliers final: 2 residues processed: 96 average time/residue: 1.3883 time to fit residues: 143.1273 Evaluate side-chains 88 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 569 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 44 optimal weight: 0.9990 chunk 91 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.076659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.059260 restraints weight = 20282.507| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.85 r_work: 0.2716 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8726 Z= 0.169 Angle : 0.539 6.840 11861 Z= 0.276 Chirality : 0.040 0.325 1388 Planarity : 0.005 0.056 1443 Dihedral : 7.317 84.493 1271 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.44 % Allowed : 13.04 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.26), residues: 1072 helix: 1.67 (0.18), residues: 797 sheet: None (None), residues: 0 loop : -0.89 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 414 HIS 0.005 0.001 HIS B 335 PHE 0.024 0.001 PHE B 251 TYR 0.023 0.001 TYR B 282 ARG 0.001 0.000 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.892 Fit side-chains REVERT: A 265 GLN cc_start: 0.9391 (mt0) cc_final: 0.9113 (mp-120) REVERT: A 295 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7392 (mtp) REVERT: B 80 THR cc_start: 0.9556 (m) cc_final: 0.9327 (p) outliers start: 13 outliers final: 2 residues processed: 99 average time/residue: 1.2171 time to fit residues: 129.0199 Evaluate side-chains 89 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 569 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 90 optimal weight: 0.0270 chunk 24 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.077042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.059706 restraints weight = 20281.820| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.86 r_work: 0.2721 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8726 Z= 0.168 Angle : 0.532 6.682 11861 Z= 0.270 Chirality : 0.040 0.323 1388 Planarity : 0.005 0.056 1443 Dihedral : 7.122 76.689 1271 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.55 % Allowed : 13.59 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.26), residues: 1072 helix: 1.71 (0.18), residues: 797 sheet: None (None), residues: 0 loop : -0.85 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 414 HIS 0.004 0.001 HIS B 335 PHE 0.024 0.001 PHE B 251 TYR 0.023 0.001 TYR B 282 ARG 0.001 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.983 Fit side-chains REVERT: A 265 GLN cc_start: 0.9397 (mt0) cc_final: 0.9100 (mp-120) REVERT: A 295 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7687 (mtt) REVERT: B 80 THR cc_start: 0.9579 (m) cc_final: 0.9370 (p) REVERT: B 444 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.8034 (mmm) outliers start: 14 outliers final: 5 residues processed: 97 average time/residue: 1.1059 time to fit residues: 115.8450 Evaluate side-chains 93 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain B residue 444 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 87 optimal weight: 0.6980 chunk 71 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.077263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.059844 restraints weight = 20137.323| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.86 r_work: 0.2733 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8726 Z= 0.160 Angle : 0.535 7.840 11861 Z= 0.271 Chirality : 0.040 0.320 1388 Planarity : 0.005 0.057 1443 Dihedral : 6.994 70.466 1271 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.22 % Allowed : 14.48 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.26), residues: 1072 helix: 1.72 (0.18), residues: 791 sheet: None (None), residues: 0 loop : -0.85 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 414 HIS 0.004 0.001 HIS B 335 PHE 0.023 0.001 PHE B 251 TYR 0.023 0.001 TYR B 282 ARG 0.001 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.959 Fit side-chains REVERT: A 263 THR cc_start: 0.9673 (m) cc_final: 0.9338 (p) REVERT: A 265 GLN cc_start: 0.9405 (mt0) cc_final: 0.9032 (mp10) REVERT: A 542 ILE cc_start: 0.9143 (mt) cc_final: 0.8898 (pp) REVERT: B 102 MET cc_start: 0.9087 (ptp) cc_final: 0.8850 (ptm) REVERT: B 444 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8030 (mmm) outliers start: 11 outliers final: 5 residues processed: 95 average time/residue: 1.1105 time to fit residues: 113.5630 Evaluate side-chains 93 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain B residue 444 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.1980 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 0.0050 chunk 77 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.077867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.060431 restraints weight = 20362.530| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.86 r_work: 0.2742 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8726 Z= 0.155 Angle : 0.538 10.615 11861 Z= 0.270 Chirality : 0.040 0.317 1388 Planarity : 0.005 0.057 1443 Dihedral : 6.876 64.788 1271 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.10 % Allowed : 14.92 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.26), residues: 1072 helix: 1.77 (0.18), residues: 791 sheet: None (None), residues: 0 loop : -0.81 (0.40), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 414 HIS 0.004 0.001 HIS B 335 PHE 0.023 0.001 PHE B 251 TYR 0.023 0.001 TYR B 282 ARG 0.001 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.917 Fit side-chains REVERT: A 263 THR cc_start: 0.9665 (m) cc_final: 0.9331 (p) REVERT: A 265 GLN cc_start: 0.9410 (mt0) cc_final: 0.9031 (mp10) REVERT: B 102 MET cc_start: 0.9055 (ptp) cc_final: 0.8819 (ptm) REVERT: B 444 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.8030 (mmm) outliers start: 10 outliers final: 4 residues processed: 97 average time/residue: 1.4294 time to fit residues: 149.6412 Evaluate side-chains 91 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain B residue 444 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 0.0470 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.0270 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.079024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.061149 restraints weight = 20370.960| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.91 r_work: 0.2749 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8726 Z= 0.154 Angle : 0.546 12.362 11861 Z= 0.274 Chirality : 0.039 0.313 1388 Planarity : 0.005 0.057 1443 Dihedral : 6.710 56.962 1271 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.88 % Allowed : 16.02 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.26), residues: 1072 helix: 1.79 (0.18), residues: 791 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 414 HIS 0.004 0.001 HIS B 335 PHE 0.022 0.001 PHE B 251 TYR 0.023 0.001 TYR B 282 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 1.011 Fit side-chains REVERT: B 102 MET cc_start: 0.9018 (ptp) cc_final: 0.8783 (ptm) REVERT: B 444 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.8013 (mmm) outliers start: 8 outliers final: 3 residues processed: 96 average time/residue: 1.1823 time to fit residues: 122.2250 Evaluate side-chains 89 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain B residue 444 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.078113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.060307 restraints weight = 20222.352| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.89 r_work: 0.2736 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8726 Z= 0.194 Angle : 0.575 13.427 11861 Z= 0.287 Chirality : 0.040 0.321 1388 Planarity : 0.005 0.057 1443 Dihedral : 6.685 55.363 1271 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.66 % Allowed : 16.46 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.26), residues: 1072 helix: 1.82 (0.18), residues: 791 sheet: None (None), residues: 0 loop : -0.78 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 414 HIS 0.005 0.001 HIS B 335 PHE 0.021 0.001 PHE B 251 TYR 0.023 0.001 TYR B 282 ARG 0.001 0.000 ARG A 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.894 Fit side-chains REVERT: A 265 GLN cc_start: 0.9445 (mt0) cc_final: 0.9086 (mp-120) REVERT: B 102 MET cc_start: 0.9028 (ptp) cc_final: 0.8732 (ptm) REVERT: B 444 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8062 (mmm) outliers start: 6 outliers final: 3 residues processed: 91 average time/residue: 1.1394 time to fit residues: 111.0567 Evaluate side-chains 88 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain B residue 444 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 98 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.078256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.060423 restraints weight = 20420.088| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.91 r_work: 0.2731 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8726 Z= 0.187 Angle : 0.581 13.593 11861 Z= 0.289 Chirality : 0.040 0.327 1388 Planarity : 0.005 0.057 1443 Dihedral : 6.657 54.737 1271 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.44 % Allowed : 17.02 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.26), residues: 1072 helix: 1.80 (0.18), residues: 793 sheet: None (None), residues: 0 loop : -0.76 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 414 HIS 0.006 0.001 HIS B 335 PHE 0.022 0.001 PHE B 251 TYR 0.023 0.001 TYR B 282 ARG 0.001 0.000 ARG B 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4899.20 seconds wall clock time: 86 minutes 58.42 seconds (5218.42 seconds total)