Starting phenix.real_space_refine on Wed Sep 17 11:46:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zkw_60210/09_2025/8zkw_60210.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zkw_60210/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zkw_60210/09_2025/8zkw_60210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zkw_60210/09_2025/8zkw_60210.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zkw_60210/09_2025/8zkw_60210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zkw_60210/09_2025/8zkw_60210.map" } resolution = 2.77 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= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'GLU:plan': 1} 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: 2.07, per 1000 atoms: 0.24 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: 0.81 Conformation dependent library (CDL) restraints added in 322.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.29 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: 1.15 Time building geometry restraints manager: 1.04 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 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 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: 0.970 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.750 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.380 ------------------------------------------------------------------------------- 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 8728 Z= 0.246 Angle : 0.694 10.962 11867 Z= 0.374 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 : 8.26 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 394 TYR 0.028 0.002 TYR A 282 PHE 0.024 0.001 PHE B 251 TRP 0.014 0.001 TRP B 414 HIS 0.014 0.002 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 8726) covalent geometry : angle 0.68460 (11861) hydrogen bonds : bond 0.14225 ( 573) hydrogen bonds : angle 5.48963 ( 1692) link_NAG-ASN : bond 0.01366 ( 2) link_NAG-ASN : angle 5.13542 ( 6) *********************** 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 : 0.322 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: 0.5589 time to fit residues: 52.9997 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 : 0.211 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.075689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.058054 restraints weight = 20201.015| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.84 r_work: 0.2690 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8728 Z= 0.129 Angle : 0.594 10.124 11867 Z= 0.300 Chirality : 0.042 0.332 1388 Planarity : 0.005 0.055 1443 Dihedral : 8.645 101.578 1273 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.44 % Allowed : 6.41 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.26), residues: 1072 helix: 1.37 (0.18), residues: 799 sheet: None (None), residues: 0 loop : -0.89 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 399 TYR 0.028 0.002 TYR B 282 PHE 0.026 0.001 PHE B 251 TRP 0.013 0.001 TRP B 414 HIS 0.008 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8726) covalent geometry : angle 0.58399 (11861) hydrogen bonds : bond 0.04167 ( 573) hydrogen bonds : angle 4.34387 ( 1692) link_NAG-ASN : bond 0.00953 ( 2) link_NAG-ASN : angle 4.87565 ( 6) *********************** 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 104 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.205 Fit side-chains REVERT: A 295 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8143 (mtp) REVERT: A 363 ASP cc_start: 0.8856 (m-30) cc_final: 0.8605 (m-30) REVERT: B 316 ASP cc_start: 0.8993 (p0) cc_final: 0.8678 (t70) outliers start: 13 outliers final: 3 residues processed: 93 average time/residue: 0.4976 time to fit residues: 49.6750 Evaluate side-chains 87 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 70 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 71 optimal weight: 0.0030 chunk 28 optimal weight: 0.0370 chunk 5 optimal weight: 0.0050 chunk 105 optimal weight: 0.0670 chunk 2 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 88 optimal weight: 0.0020 overall best weight: 0.0228 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.077259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.059540 restraints weight = 20032.503| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.87 r_work: 0.2726 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8728 Z= 0.114 Angle : 0.551 9.837 11867 Z= 0.278 Chirality : 0.040 0.310 1388 Planarity : 0.005 0.055 1443 Dihedral : 7.776 93.606 1271 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.22 % Allowed : 9.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.26), residues: 1072 helix: 1.48 (0.18), residues: 797 sheet: None (None), residues: 0 loop : -0.87 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 312 TYR 0.024 0.001 TYR B 282 PHE 0.026 0.001 PHE B 251 TRP 0.011 0.001 TRP A 414 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8726) covalent geometry : angle 0.54127 (11861) hydrogen bonds : bond 0.03638 ( 573) hydrogen bonds : angle 4.16646 ( 1692) link_NAG-ASN : bond 0.00912 ( 2) link_NAG-ASN : angle 4.66121 ( 6) *********************** 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 101 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.335 Fit side-chains REVERT: A 295 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.7621 (mtp) REVERT: A 363 ASP cc_start: 0.8884 (m-30) cc_final: 0.8637 (m-30) REVERT: A 374 MET cc_start: 0.8664 (tmm) cc_final: 0.8301 (tmm) outliers start: 11 outliers final: 3 residues processed: 93 average time/residue: 0.5374 time to fit residues: 53.6738 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 : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP 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 85 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 52 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 0.0070 chunk 84 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.3243 r_free = 0.3243 target = 0.077190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.059608 restraints weight = 20504.462| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.89 r_work: 0.2733 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8728 Z= 0.110 Angle : 0.539 9.317 11867 Z= 0.271 Chirality : 0.039 0.316 1388 Planarity : 0.005 0.056 1443 Dihedral : 7.404 84.461 1271 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.99 % Allowed : 10.72 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.26), residues: 1072 helix: 1.54 (0.18), residues: 799 sheet: None (None), residues: 0 loop : -0.84 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 371 TYR 0.023 0.001 TYR B 282 PHE 0.025 0.001 PHE B 251 TRP 0.010 0.001 TRP B 414 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8726) covalent geometry : angle 0.52928 (11861) hydrogen bonds : bond 0.03456 ( 573) hydrogen bonds : angle 4.06018 ( 1692) link_NAG-ASN : bond 0.00872 ( 2) link_NAG-ASN : angle 4.45410 ( 6) *********************** 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 108 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.360 Fit side-chains REVERT: A 295 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.7664 (mtt) REVERT: A 363 ASP cc_start: 0.8924 (m-30) cc_final: 0.8673 (m-30) REVERT: A 374 MET cc_start: 0.8719 (tmm) cc_final: 0.8425 (tmm) outliers start: 18 outliers final: 4 residues processed: 96 average time/residue: 0.5107 time to fit residues: 52.6976 Evaluate side-chains 88 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 323 ASP Chi-restraints excluded: chain A residue 332 MET 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 40 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 = 0.3213 r_free = 0.3213 target = 0.075709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.058218 restraints weight = 20637.298| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.87 r_work: 0.2687 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8728 Z= 0.151 Angle : 0.564 9.016 11867 Z= 0.285 Chirality : 0.041 0.326 1388 Planarity : 0.005 0.053 1443 Dihedral : 7.264 78.924 1271 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.10 % Allowed : 12.27 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.26), residues: 1072 helix: 1.63 (0.18), residues: 799 sheet: None (None), residues: 0 loop : -0.85 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 258 TYR 0.022 0.001 TYR B 282 PHE 0.025 0.001 PHE B 251 TRP 0.012 0.001 TRP B 414 HIS 0.006 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8726) covalent geometry : angle 0.55546 (11861) hydrogen bonds : bond 0.03684 ( 573) hydrogen bonds : angle 4.07365 ( 1692) link_NAG-ASN : bond 0.00850 ( 2) link_NAG-ASN : angle 4.35400 ( 6) *********************** 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 97 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.346 Fit side-chains REVERT: A 265 GLN cc_start: 0.9385 (mt0) cc_final: 0.9108 (mp-120) REVERT: A 295 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.7827 (mtm) REVERT: A 363 ASP cc_start: 0.8921 (m-30) cc_final: 0.8676 (m-30) REVERT: A 374 MET cc_start: 0.8765 (tmm) cc_final: 0.8435 (tmm) outliers start: 10 outliers final: 4 residues processed: 90 average time/residue: 0.5733 time to fit residues: 55.3014 Evaluate side-chains 89 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 332 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 28 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3224 r_free = 0.3224 target = 0.076266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.058785 restraints weight = 20338.034| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.85 r_work: 0.2699 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8728 Z= 0.131 Angle : 0.550 8.930 11867 Z= 0.276 Chirality : 0.040 0.322 1388 Planarity : 0.005 0.053 1443 Dihedral : 7.135 73.018 1271 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.22 % Allowed : 12.93 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.26), residues: 1072 helix: 1.64 (0.18), residues: 799 sheet: None (None), residues: 0 loop : -0.83 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 371 TYR 0.022 0.001 TYR B 282 PHE 0.024 0.001 PHE B 251 TRP 0.012 0.001 TRP B 414 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8726) covalent geometry : angle 0.54136 (11861) hydrogen bonds : bond 0.03538 ( 573) hydrogen bonds : angle 4.01936 ( 1692) link_NAG-ASN : bond 0.00836 ( 2) link_NAG-ASN : angle 4.31675 ( 6) *********************** 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 100 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.364 Fit side-chains REVERT: A 265 GLN cc_start: 0.9400 (mt0) cc_final: 0.9060 (mp10) REVERT: A 295 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.7749 (mtt) REVERT: A 363 ASP cc_start: 0.8917 (m-30) cc_final: 0.8664 (m-30) REVERT: B 80 THR cc_start: 0.9578 (m) cc_final: 0.9324 (p) outliers start: 11 outliers final: 3 residues processed: 93 average time/residue: 0.5250 time to fit residues: 52.4811 Evaluate side-chains 90 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 18 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 95 optimal weight: 0.0870 chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3185 r_free = 0.3185 target = 0.076148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.058330 restraints weight = 20543.651| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.92 r_work: 0.2717 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8728 Z= 0.114 Angle : 0.548 8.847 11867 Z= 0.275 Chirality : 0.040 0.318 1388 Planarity : 0.005 0.053 1443 Dihedral : 6.990 67.318 1271 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.88 % Allowed : 14.03 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.26), residues: 1072 helix: 1.68 (0.18), residues: 799 sheet: None (None), residues: 0 loop : -0.81 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 371 TYR 0.022 0.001 TYR B 282 PHE 0.024 0.001 PHE B 251 TRP 0.011 0.001 TRP B 414 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8726) covalent geometry : angle 0.53980 (11861) hydrogen bonds : bond 0.03430 ( 573) hydrogen bonds : angle 3.98383 ( 1692) link_NAG-ASN : bond 0.00829 ( 2) link_NAG-ASN : angle 4.27060 ( 6) *********************** 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: 8 poor density : 92 time to evaluate : 0.361 Fit side-chains REVERT: A 265 GLN cc_start: 0.9408 (mt0) cc_final: 0.9028 (mp10) REVERT: A 295 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.7790 (mtm) REVERT: A 363 ASP cc_start: 0.8942 (m-30) cc_final: 0.8678 (m-30) REVERT: A 542 ILE cc_start: 0.8889 (tp) cc_final: 0.8389 (pp) REVERT: B 80 THR cc_start: 0.9584 (m) cc_final: 0.9340 (p) REVERT: B 102 MET cc_start: 0.9085 (ptp) cc_final: 0.8860 (ptm) outliers start: 8 outliers final: 3 residues processed: 96 average time/residue: 0.5445 time to fit residues: 56.1149 Evaluate side-chains 93 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3180 r_free = 0.3180 target = 0.075807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.057953 restraints weight = 20384.030| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.89 r_work: 0.2701 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8728 Z= 0.127 Angle : 0.564 9.342 11867 Z= 0.280 Chirality : 0.040 0.319 1388 Planarity : 0.005 0.055 1443 Dihedral : 6.920 63.228 1271 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.55 % Allowed : 14.36 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.26), residues: 1072 helix: 1.70 (0.18), residues: 799 sheet: None (None), residues: 0 loop : -0.81 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 325 TYR 0.022 0.001 TYR B 282 PHE 0.023 0.001 PHE B 251 TRP 0.011 0.001 TRP B 414 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8726) covalent geometry : angle 0.55649 (11861) hydrogen bonds : bond 0.03480 ( 573) hydrogen bonds : angle 3.99294 ( 1692) link_NAG-ASN : bond 0.00834 ( 2) link_NAG-ASN : angle 4.24183 ( 6) *********************** 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 94 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.359 Fit side-chains REVERT: A 265 GLN cc_start: 0.9410 (mt0) cc_final: 0.9018 (mp10) REVERT: A 295 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.7814 (mtm) REVERT: A 363 ASP cc_start: 0.8949 (m-30) cc_final: 0.8684 (m-30) REVERT: A 539 ASP cc_start: 0.8635 (m-30) cc_final: 0.8432 (m-30) REVERT: A 542 ILE cc_start: 0.8882 (tp) cc_final: 0.8375 (pp) REVERT: B 80 THR cc_start: 0.9594 (m) cc_final: 0.9355 (p) REVERT: B 102 MET cc_start: 0.9061 (ptp) cc_final: 0.8833 (ptm) outliers start: 5 outliers final: 2 residues processed: 92 average time/residue: 0.5838 time to fit residues: 57.5714 Evaluate side-chains 91 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 569 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.0030 chunk 45 optimal weight: 0.0980 chunk 77 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.078249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.060596 restraints weight = 20143.493| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.88 r_work: 0.2743 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8728 Z= 0.111 Angle : 0.557 11.835 11867 Z= 0.277 Chirality : 0.039 0.312 1388 Planarity : 0.005 0.056 1443 Dihedral : 6.732 55.521 1271 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.66 % Allowed : 15.14 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.26), residues: 1072 helix: 1.74 (0.18), residues: 797 sheet: None (None), residues: 0 loop : -0.79 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 353 TYR 0.023 0.001 TYR B 282 PHE 0.022 0.001 PHE B 251 TRP 0.010 0.001 TRP B 414 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8726) covalent geometry : angle 0.54906 (11861) hydrogen bonds : bond 0.03298 ( 573) hydrogen bonds : angle 3.95865 ( 1692) link_NAG-ASN : bond 0.00835 ( 2) link_NAG-ASN : angle 4.18881 ( 6) *********************** 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 102 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.383 Fit side-chains REVERT: A 263 THR cc_start: 0.9668 (m) cc_final: 0.9311 (p) REVERT: A 265 GLN cc_start: 0.9406 (mt0) cc_final: 0.9078 (mp-120) REVERT: A 363 ASP cc_start: 0.8954 (m-30) cc_final: 0.8686 (m-30) REVERT: A 542 ILE cc_start: 0.8926 (tp) cc_final: 0.8434 (pp) REVERT: B 80 THR cc_start: 0.9593 (m) cc_final: 0.9374 (p) REVERT: B 102 MET cc_start: 0.9006 (ptp) cc_final: 0.8773 (ptm) outliers start: 6 outliers final: 2 residues processed: 99 average time/residue: 0.5356 time to fit residues: 56.9242 Evaluate side-chains 92 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 569 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 0.0770 chunk 102 optimal weight: 0.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- 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 = 0.3188 r_free = 0.3188 target = 0.076430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.058547 restraints weight = 20380.572| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.91 r_work: 0.2725 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8728 Z= 0.125 Angle : 0.574 13.548 11867 Z= 0.285 Chirality : 0.040 0.313 1388 Planarity : 0.005 0.055 1443 Dihedral : 6.702 54.562 1271 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.33 % Allowed : 15.91 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.26), residues: 1072 helix: 1.79 (0.18), residues: 799 sheet: None (None), residues: 0 loop : -0.79 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 325 TYR 0.023 0.001 TYR B 282 PHE 0.022 0.001 PHE B 251 TRP 0.010 0.001 TRP B 414 HIS 0.005 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8726) covalent geometry : angle 0.56626 (11861) hydrogen bonds : bond 0.03415 ( 573) hydrogen bonds : angle 3.96712 ( 1692) link_NAG-ASN : bond 0.00836 ( 2) link_NAG-ASN : angle 4.18893 ( 6) ********************** 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 94 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 91 time to evaluate : 0.353 Fit side-chains REVERT: A 363 ASP cc_start: 0.8952 (m-30) cc_final: 0.8682 (m-30) REVERT: A 542 ILE cc_start: 0.8962 (tp) cc_final: 0.8470 (pp) REVERT: B 52 LEU cc_start: 0.9302 (mm) cc_final: 0.9099 (mm) REVERT: B 80 THR cc_start: 0.9591 (m) cc_final: 0.9370 (p) REVERT: B 102 MET cc_start: 0.8983 (ptp) cc_final: 0.8691 (ptm) outliers start: 3 outliers final: 2 residues processed: 93 average time/residue: 0.5590 time to fit residues: 55.7976 Evaluate side-chains 90 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 569 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 104 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 95 optimal weight: 0.0870 chunk 48 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3256 r_free = 0.3256 target = 0.078529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.061065 restraints weight = 19981.394| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.86 r_work: 0.2749 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8728 Z= 0.115 Angle : 0.584 13.631 11867 Z= 0.289 Chirality : 0.040 0.320 1388 Planarity : 0.005 0.056 1443 Dihedral : 6.607 53.138 1271 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.44 % Allowed : 16.13 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.26), residues: 1072 helix: 1.81 (0.18), residues: 797 sheet: None (None), residues: 0 loop : -0.81 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 353 TYR 0.023 0.001 TYR B 282 PHE 0.022 0.001 PHE B 251 TRP 0.010 0.001 TRP B 414 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8726) covalent geometry : angle 0.57605 (11861) hydrogen bonds : bond 0.03318 ( 573) hydrogen bonds : angle 3.94660 ( 1692) link_NAG-ASN : bond 0.01084 ( 2) link_NAG-ASN : angle 4.20645 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2461.68 seconds wall clock time: 42 minutes 53.25 seconds (2573.25 seconds total)