Starting phenix.real_space_refine on Thu Mar 6 03:53:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgt_43224/03_2025/8vgt_43224.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgt_43224/03_2025/8vgt_43224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vgt_43224/03_2025/8vgt_43224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgt_43224/03_2025/8vgt_43224.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgt_43224/03_2025/8vgt_43224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgt_43224/03_2025/8vgt_43224.cif" } resolution = 2.9 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= -0.000 sd= 0.126 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: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 3014 2.51 5 N 823 2.21 5 O 830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4714 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2040 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 7, 'GLU:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2604 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 331} Chain breaks: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 1, 'GLU:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.65, per 1000 atoms: 0.77 Number of scatterers: 4714 At special positions: 0 Unit cell: (78, 83, 120, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 830 8.00 N 823 7.00 C 3014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.02 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.11 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 605 " distance=2.04 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.11 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 567 " distance=2.02 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.02 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.05 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.08 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 569 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 588 " distance=2.02 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 148 " distance=2.02 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 231 " distance=2.00 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 241 " distance=2.04 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 365 " distance=2.05 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 297 " distance=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 465 " distance=2.13 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 BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 701 " - " ASN A 454 " " NAG A 702 " - " ASN A 470 " " NAG A 703 " - " ASN A 433 " " NAG C 1 " - " ASN B 213 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 605.1 milliseconds 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1168 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 12 sheets defined 16.1% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.582A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 344 removed outlier: 3.740A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 394 through 402 removed outlier: 3.955A pdb=" N ARG A 398 " --> pdb=" O ASN A 395 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER A 399 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 removed outlier: 3.525A pdb=" N ASN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.581A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 220 through 223 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.929A pdb=" N GLU B 299 " --> pdb=" O HIS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 477 through 490 removed outlier: 5.418A pdb=" N ASP B 482 " --> pdb=" O MET B 478 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TRP B 483 " --> pdb=" O VAL B 479 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.737A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.578A pdb=" N SER A 422 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N SER A 428 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N THR A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 349 Processing sheet with id=AA4, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AA5, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.251A pdb=" N CYS A 466 " --> pdb=" O SER A 538 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AA7, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 152 Processing sheet with id=AA9, first strand: chain 'B' and resid 196 through 200 Processing sheet with id=AB1, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AB2, first strand: chain 'B' and resid 260 through 261 removed outlier: 4.170A pdb=" N CYS B 426 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLY B 475 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR B 459 " --> pdb=" O GLY B 475 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU B 445 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N SER B 382 " --> pdb=" O PRO B 444 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER B 448 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 378 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 270 through 275 removed outlier: 6.110A pdb=" N VAL B 275 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N HIS B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU B 348 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL B 331 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS B 350 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TRP B 308 " --> pdb=" O VAL B 328 " (cutoff:3.500A) 143 hydrogen bonds defined for protein. 351 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: 1.30 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1202 1.33 - 1.46: 1377 1.46 - 1.59: 2206 1.59 - 1.72: 0 1.72 - 1.85: 56 Bond restraints: 4841 Sorted by residual: bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.473 -0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" N VAL A 509 " pdb=" CA VAL A 509 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.50e+00 bond pdb=" CD GLU A 345 " pdb=" OE2 GLU A 345 " ideal model delta sigma weight residual 1.249 1.199 0.050 1.90e-02 2.77e+03 6.98e+00 bond pdb=" CG ASP B 345 " pdb=" OD2 ASP B 345 " ideal model delta sigma weight residual 1.249 1.200 0.049 1.90e-02 2.77e+03 6.60e+00 bond pdb=" N ALA B 230 " pdb=" CA ALA B 230 " ideal model delta sigma weight residual 1.457 1.487 -0.031 1.20e-02 6.94e+03 6.50e+00 ... (remaining 4836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 5693 1.68 - 3.35: 733 3.35 - 5.03: 110 5.03 - 6.70: 56 6.70 - 8.38: 16 Bond angle restraints: 6608 Sorted by residual: angle pdb=" C GLY B 153 " pdb=" N PRO B 154 " pdb=" CA PRO B 154 " ideal model delta sigma weight residual 119.56 127.94 -8.38 1.02e+00 9.61e-01 6.75e+01 angle pdb=" C TRP B 267 " pdb=" N PRO B 268 " pdb=" CA PRO B 268 " ideal model delta sigma weight residual 119.56 127.72 -8.16 1.02e+00 9.61e-01 6.39e+01 angle pdb=" C ASP A 529 " pdb=" N PRO A 530 " pdb=" CA PRO A 530 " ideal model delta sigma weight residual 119.56 127.37 -7.81 1.02e+00 9.61e-01 5.87e+01 angle pdb=" C ASP A 523 " pdb=" N PRO A 524 " pdb=" CA PRO A 524 " ideal model delta sigma weight residual 119.82 126.98 -7.16 9.80e-01 1.04e+00 5.34e+01 angle pdb=" C PRO A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta sigma weight residual 119.76 127.15 -7.39 1.03e+00 9.43e-01 5.15e+01 ... (remaining 6603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 2777 17.86 - 35.72: 111 35.72 - 53.58: 21 53.58 - 71.44: 9 71.44 - 89.30: 3 Dihedral angle restraints: 2921 sinusoidal: 1103 harmonic: 1818 Sorted by residual: dihedral pdb=" CB CYS B 410 " pdb=" SG CYS B 410 " pdb=" SG CYS B 426 " pdb=" CB CYS B 426 " ideal model delta sinusoidal sigma weight residual -86.00 -162.51 76.51 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS B 437 " pdb=" SG CYS B 437 " pdb=" SG CYS B 465 " pdb=" CB CYS B 465 " ideal model delta sinusoidal sigma weight residual -86.00 -136.59 50.59 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS A 466 " pdb=" SG CYS A 466 " pdb=" SG CYS A 546 " pdb=" CB CYS A 546 " ideal model delta sinusoidal sigma weight residual -86.00 -128.95 42.95 1 1.00e+01 1.00e-02 2.57e+01 ... (remaining 2918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 486 0.064 - 0.128: 183 0.128 - 0.192: 44 0.192 - 0.256: 10 0.256 - 0.320: 5 Chirality restraints: 728 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.34e+01 chirality pdb=" C2 NAG A 702 " pdb=" C1 NAG A 702 " pdb=" C3 NAG A 702 " pdb=" N2 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C2 NAG A 703 " pdb=" C1 NAG A 703 " pdb=" C3 NAG A 703 " pdb=" N2 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.49 -2.79 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 725 not shown) Planarity restraints: 857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 485 " 0.033 2.00e-02 2.50e+03 1.99e-02 7.92e+00 pdb=" CG TYR B 485 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 485 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 485 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 485 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR B 485 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 485 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 485 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 582 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C CYS A 582 " 0.045 2.00e-02 2.50e+03 pdb=" O CYS A 582 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A 583 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 277 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C ASN B 277 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN B 277 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 278 " 0.011 2.00e-02 2.50e+03 ... (remaining 854 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 1742 2.88 - 3.38: 4019 3.38 - 3.89: 7811 3.89 - 4.39: 9370 4.39 - 4.90: 15390 Nonbonded interactions: 38332 Sorted by model distance: nonbonded pdb=" O SER B 137 " pdb=" N CYS B 139 " model vdw 2.374 3.120 nonbonded pdb=" O TRP B 483 " pdb=" NE2 GLN B 487 " model vdw 2.495 3.120 nonbonded pdb=" OD1 ASP A 417 " pdb=" N THR A 418 " model vdw 2.507 3.120 nonbonded pdb=" N ASP B 144 " pdb=" OD1 ASP B 144 " model vdw 2.522 3.120 nonbonded pdb=" O ASP B 458 " pdb=" OD1 ASP B 458 " model vdw 2.525 3.040 ... (remaining 38327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 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 : 0.011 0.060 4841 Z= 0.722 Angle : 1.299 8.377 6608 Z= 0.889 Chirality : 0.074 0.320 728 Planarity : 0.005 0.026 853 Dihedral : 10.509 89.304 1696 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.48 % Allowed : 3.88 % Favored : 95.64 % Rotamer: Outliers : 0.70 % Allowed : 3.02 % Favored : 96.28 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 6.67 % 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: -0.41 (0.32), residues: 619 helix: -2.23 (0.45), residues: 83 sheet: 0.52 (0.43), residues: 137 loop : -0.04 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP B 267 HIS 0.008 0.002 HIS A 512 PHE 0.021 0.004 PHE A 450 TYR 0.035 0.004 TYR B 485 ARG 0.005 0.001 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.535 Fit side-chains REVERT: A 536 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8020 (mmtp) REVERT: B 350 LYS cc_start: 0.8660 (tttm) cc_final: 0.8453 (tttp) REVERT: B 424 MET cc_start: 0.8786 (mtt) cc_final: 0.8555 (mtt) outliers start: 3 outliers final: 1 residues processed: 101 average time/residue: 1.1450 time to fit residues: 120.5422 Evaluate side-chains 58 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain B residue 212 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 31 optimal weight: 0.0470 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN A 343 ASN A 458 HIS ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS B 334 HIS B 343 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.184366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.157392 restraints weight = 4661.080| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.89 r_work: 0.3622 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4841 Z= 0.210 Angle : 0.608 6.631 6608 Z= 0.321 Chirality : 0.049 0.315 728 Planarity : 0.005 0.037 853 Dihedral : 5.632 55.948 782 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.40 % Allowed : 11.16 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.29 (0.32), residues: 619 helix: -1.26 (0.56), residues: 76 sheet: 0.70 (0.47), residues: 113 loop : -0.19 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 384 HIS 0.006 0.002 HIS B 334 PHE 0.016 0.002 PHE A 594 TYR 0.010 0.001 TYR A 427 ARG 0.006 0.001 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.506 Fit side-chains REVERT: A 334 ASN cc_start: 0.7746 (m110) cc_final: 0.7216 (m-40) REVERT: A 486 LYS cc_start: 0.8535 (mttt) cc_final: 0.8129 (mtpp) REVERT: A 544 GLU cc_start: 0.8206 (pt0) cc_final: 0.7887 (pt0) REVERT: B 147 ARG cc_start: 0.7474 (mmm160) cc_final: 0.6981 (mmm160) REVERT: B 395 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.6904 (tp30) outliers start: 6 outliers final: 2 residues processed: 69 average time/residue: 1.0136 time to fit residues: 73.3491 Evaluate side-chains 60 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 395 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.0060 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.5774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.181414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154074 restraints weight = 4719.460| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.90 r_work: 0.3581 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4841 Z= 0.220 Angle : 0.555 6.464 6608 Z= 0.295 Chirality : 0.048 0.303 728 Planarity : 0.005 0.040 853 Dihedral : 4.517 32.312 778 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 2.33 % Allowed : 11.16 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.18 (0.33), residues: 619 helix: -0.96 (0.57), residues: 76 sheet: 0.04 (0.42), residues: 142 loop : 0.10 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 384 HIS 0.005 0.001 HIS A 488 PHE 0.016 0.002 PHE A 594 TYR 0.009 0.001 TYR B 414 ARG 0.003 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.470 Fit side-chains REVERT: A 486 LYS cc_start: 0.8664 (mttt) cc_final: 0.8277 (mtpp) REVERT: B 147 ARG cc_start: 0.7493 (mmm160) cc_final: 0.7145 (mmm160) REVERT: B 388 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7067 (pt0) REVERT: B 395 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.6865 (tp30) outliers start: 10 outliers final: 5 residues processed: 68 average time/residue: 0.9838 time to fit residues: 70.2199 Evaluate side-chains 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 437 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.0570 chunk 55 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.180216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.152664 restraints weight = 4727.646| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.90 r_work: 0.3573 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4841 Z= 0.219 Angle : 0.548 7.018 6608 Z= 0.292 Chirality : 0.048 0.342 728 Planarity : 0.005 0.042 853 Dihedral : 4.485 33.340 778 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 2.79 % Allowed : 11.86 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.19 (0.33), residues: 619 helix: -0.83 (0.59), residues: 76 sheet: -0.07 (0.42), residues: 142 loop : 0.11 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 384 HIS 0.005 0.001 HIS A 488 PHE 0.015 0.001 PHE A 594 TYR 0.011 0.001 TYR B 226 ARG 0.003 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 486 LYS cc_start: 0.8703 (mttt) cc_final: 0.8286 (mtpp) REVERT: B 147 ARG cc_start: 0.7371 (mmm160) cc_final: 0.7059 (mmm160) REVERT: B 227 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.7520 (m90) REVERT: B 388 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7071 (pt0) REVERT: B 395 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.6866 (tp30) REVERT: B 424 MET cc_start: 0.8750 (mtt) cc_final: 0.8473 (mtt) outliers start: 12 outliers final: 6 residues processed: 68 average time/residue: 0.9724 time to fit residues: 69.5039 Evaluate side-chains 69 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 437 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.0870 chunk 41 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.181020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.153387 restraints weight = 4738.408| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.90 r_work: 0.3597 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4841 Z= 0.187 Angle : 0.515 7.477 6608 Z= 0.275 Chirality : 0.047 0.331 728 Planarity : 0.004 0.043 853 Dihedral : 4.355 35.178 778 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.79 % Allowed : 12.33 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.14 (0.33), residues: 619 helix: -0.72 (0.61), residues: 76 sheet: -0.14 (0.42), residues: 142 loop : 0.17 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 306 HIS 0.004 0.001 HIS A 488 PHE 0.014 0.001 PHE A 594 TYR 0.008 0.001 TYR B 414 ARG 0.002 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 486 LYS cc_start: 0.8686 (mttt) cc_final: 0.8259 (mtpp) REVERT: B 147 ARG cc_start: 0.7245 (mmm160) cc_final: 0.6952 (mmm160) REVERT: B 227 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.7442 (m90) REVERT: B 388 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7045 (pt0) REVERT: B 395 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.6838 (tp30) outliers start: 12 outliers final: 7 residues processed: 71 average time/residue: 1.0765 time to fit residues: 80.0689 Evaluate side-chains 72 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 437 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.174154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.141826 restraints weight = 4663.966| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.09 r_work: 0.3513 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4841 Z= 0.226 Angle : 0.545 8.536 6608 Z= 0.287 Chirality : 0.048 0.324 728 Planarity : 0.005 0.044 853 Dihedral : 4.416 36.289 778 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.26 % Allowed : 12.33 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.25 (0.34), residues: 619 helix: -0.93 (0.59), residues: 77 sheet: -0.23 (0.42), residues: 142 loop : 0.13 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 306 HIS 0.005 0.002 HIS A 488 PHE 0.012 0.001 PHE A 594 TYR 0.009 0.001 TYR B 414 ARG 0.002 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8285 (mp) cc_final: 0.7980 (mp) REVERT: A 486 LYS cc_start: 0.8670 (mttt) cc_final: 0.8212 (mtpp) REVERT: A 589 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.6462 (m-40) REVERT: B 227 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.7513 (m90) REVERT: B 388 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6988 (pt0) REVERT: B 395 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.6955 (tp30) REVERT: B 424 MET cc_start: 0.8642 (mtt) cc_final: 0.8336 (mtt) outliers start: 14 outliers final: 9 residues processed: 65 average time/residue: 0.9265 time to fit residues: 63.4388 Evaluate side-chains 71 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 437 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.174420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.142494 restraints weight = 4608.477| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.05 r_work: 0.3524 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4841 Z= 0.214 Angle : 0.537 8.528 6608 Z= 0.281 Chirality : 0.048 0.324 728 Planarity : 0.004 0.045 853 Dihedral : 4.336 36.968 778 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.79 % Allowed : 13.49 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.22 (0.34), residues: 619 helix: -0.92 (0.59), residues: 77 sheet: -0.18 (0.43), residues: 142 loop : 0.14 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 306 HIS 0.004 0.001 HIS A 488 PHE 0.011 0.001 PHE A 594 TYR 0.009 0.001 TYR B 414 ARG 0.003 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 486 LYS cc_start: 0.8637 (mttt) cc_final: 0.8163 (mtpp) REVERT: A 589 ASN cc_start: 0.7381 (OUTLIER) cc_final: 0.6316 (m-40) REVERT: B 227 HIS cc_start: 0.8184 (OUTLIER) cc_final: 0.7461 (m90) REVERT: B 388 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6963 (pt0) REVERT: B 395 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.6892 (tp30) outliers start: 12 outliers final: 8 residues processed: 67 average time/residue: 0.9116 time to fit residues: 64.4698 Evaluate side-chains 71 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 437 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.170483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.138314 restraints weight = 4630.222| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.06 r_work: 0.3474 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4841 Z= 0.346 Angle : 0.612 8.023 6608 Z= 0.320 Chirality : 0.050 0.323 728 Planarity : 0.005 0.045 853 Dihedral : 4.696 37.301 778 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.49 % Allowed : 12.79 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.38 (0.34), residues: 619 helix: -1.18 (0.57), residues: 77 sheet: -0.21 (0.43), residues: 142 loop : 0.03 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 306 HIS 0.006 0.002 HIS A 488 PHE 0.013 0.002 PHE B 319 TYR 0.012 0.002 TYR B 414 ARG 0.003 0.001 ARG B 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 486 LYS cc_start: 0.8688 (mttt) cc_final: 0.8232 (mtpt) REVERT: A 589 ASN cc_start: 0.7493 (OUTLIER) cc_final: 0.6472 (m-40) REVERT: B 388 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7037 (pt0) REVERT: B 395 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7018 (tp30) outliers start: 15 outliers final: 7 residues processed: 67 average time/residue: 1.0285 time to fit residues: 72.7314 Evaluate side-chains 68 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 437 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 40 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.173078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.140991 restraints weight = 4628.314| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.07 r_work: 0.3502 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4841 Z= 0.219 Angle : 0.547 8.098 6608 Z= 0.288 Chirality : 0.048 0.322 728 Planarity : 0.005 0.046 853 Dihedral : 4.471 37.554 778 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.56 % Allowed : 13.95 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.33 (0.34), residues: 619 helix: -1.06 (0.58), residues: 77 sheet: -0.22 (0.43), residues: 142 loop : 0.06 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 306 HIS 0.004 0.001 HIS A 488 PHE 0.011 0.001 PHE A 594 TYR 0.009 0.001 TYR B 414 ARG 0.004 0.000 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 486 LYS cc_start: 0.8687 (mttt) cc_final: 0.8234 (mtpt) REVERT: A 589 ASN cc_start: 0.7434 (OUTLIER) cc_final: 0.6387 (m-40) REVERT: B 227 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.7514 (m90) REVERT: B 388 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6973 (pt0) REVERT: B 395 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.6914 (tp30) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 1.1545 time to fit residues: 78.3801 Evaluate side-chains 70 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 437 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.173087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140853 restraints weight = 4643.255| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.08 r_work: 0.3502 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4841 Z= 0.229 Angle : 0.550 8.173 6608 Z= 0.288 Chirality : 0.048 0.318 728 Planarity : 0.005 0.046 853 Dihedral : 4.424 37.647 778 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.79 % Allowed : 13.95 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.30 (0.34), residues: 619 helix: -1.06 (0.58), residues: 77 sheet: -0.21 (0.43), residues: 142 loop : 0.10 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 306 HIS 0.004 0.001 HIS A 488 PHE 0.011 0.001 PHE A 594 TYR 0.009 0.001 TYR B 414 ARG 0.004 0.000 ARG B 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 486 LYS cc_start: 0.8748 (mttt) cc_final: 0.8245 (mtpt) REVERT: A 589 ASN cc_start: 0.7385 (OUTLIER) cc_final: 0.6366 (m-40) REVERT: B 227 HIS cc_start: 0.8181 (OUTLIER) cc_final: 0.7530 (m90) REVERT: B 388 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6960 (pt0) REVERT: B 395 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.6932 (tp30) outliers start: 12 outliers final: 8 residues processed: 62 average time/residue: 1.0141 time to fit residues: 66.4047 Evaluate side-chains 69 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 437 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.170476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.138257 restraints weight = 4729.826| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.08 r_work: 0.3470 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4841 Z= 0.342 Angle : 0.608 8.145 6608 Z= 0.318 Chirality : 0.050 0.318 728 Planarity : 0.005 0.045 853 Dihedral : 4.683 37.118 778 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.49 % Allowed : 13.26 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.45 (0.34), residues: 619 helix: -1.26 (0.56), residues: 77 sheet: -0.24 (0.43), residues: 142 loop : -0.02 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 306 HIS 0.006 0.002 HIS A 488 PHE 0.012 0.002 PHE B 319 TYR 0.011 0.002 TYR B 414 ARG 0.004 0.001 ARG B 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3955.59 seconds wall clock time: 69 minutes 41.08 seconds (4181.08 seconds total)