Starting phenix.real_space_refine on Sat May 10 02:51:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgt_43224/05_2025/8vgt_43224.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgt_43224/05_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_43224/05_2025/8vgt_43224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgt_43224/05_2025/8vgt_43224.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgt_43224/05_2025/8vgt_43224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgt_43224/05_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-5687/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: 3.43, per 1000 atoms: 0.73 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: 1.10 Conformation dependent library (CDL) restraints added in 549.1 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: 0.58 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: 1.28 Time building geometry restraints manager: 1.32 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.790 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: 0.000 Load rotamer database and sin/cos tables:12.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- 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 0.096 4865 Z= 0.622 Angle : 1.349 14.283 6661 Z= 0.903 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 Details of bonding type rmsd link_NAG-ASN : bond 0.05612 ( 4) link_NAG-ASN : angle 1.85987 ( 12) link_BETA1-4 : bond 0.04592 ( 1) link_BETA1-4 : angle 2.32085 ( 3) hydrogen bonds : bond 0.17926 ( 137) hydrogen bonds : angle 8.82028 ( 351) SS BOND : bond 0.03699 ( 19) SS BOND : angle 4.88900 ( 38) covalent geometry : bond 0.01085 ( 4841) covalent geometry : angle 1.29917 ( 6608) *********************** 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 : 0.490 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: 1.1309 time to fit residues: 118.9642 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 : 0.619 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 0.0470 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 A 512 HIS B 307 HIS B 334 HIS B 343 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.182222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155106 restraints weight = 4675.412| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.89 r_work: 0.3600 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4865 Z= 0.166 Angle : 0.638 6.539 6661 Z= 0.337 Chirality : 0.050 0.311 728 Planarity : 0.005 0.037 853 Dihedral : 5.541 57.144 782 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.40 % Allowed : 11.40 % Favored : 87.21 % 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: -0.23 (0.32), residues: 619 helix: -1.25 (0.56), residues: 76 sheet: 0.72 (0.47), residues: 118 loop : -0.15 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 384 HIS 0.007 0.002 HIS B 334 PHE 0.017 0.002 PHE A 594 TYR 0.009 0.001 TYR B 414 ARG 0.006 0.001 ARG A 587 Details of bonding type rmsd link_NAG-ASN : bond 0.01466 ( 4) link_NAG-ASN : angle 2.13425 ( 12) link_BETA1-4 : bond 0.01018 ( 1) link_BETA1-4 : angle 1.10946 ( 3) hydrogen bonds : bond 0.04788 ( 137) hydrogen bonds : angle 6.23573 ( 351) SS BOND : bond 0.00545 ( 19) SS BOND : angle 1.30271 ( 38) covalent geometry : bond 0.00380 ( 4841) covalent geometry : angle 0.62617 ( 6608) *********************** 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 70 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.523 Fit side-chains REVERT: A 486 LYS cc_start: 0.8525 (mttt) cc_final: 0.8128 (mtpp) REVERT: A 544 GLU cc_start: 0.8418 (pt0) cc_final: 0.8107 (pt0) REVERT: B 147 ARG cc_start: 0.7387 (mmm160) cc_final: 0.6999 (mmm160) REVERT: B 388 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6954 (pt0) REVERT: B 395 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.6914 (tp30) outliers start: 6 outliers final: 2 residues processed: 67 average time/residue: 1.0312 time to fit residues: 72.4727 Evaluate side-chains 59 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 388 GLU 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: 0.0980 chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 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 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.179352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151911 restraints weight = 4725.406| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.91 r_work: 0.3559 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4865 Z= 0.164 Angle : 0.614 8.201 6661 Z= 0.319 Chirality : 0.049 0.318 728 Planarity : 0.005 0.040 853 Dihedral : 4.627 32.467 778 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.26 % Favored : 97.58 % Rotamer: Outliers : 2.56 % Allowed : 11.86 % Favored : 85.58 % 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: -0.23 (0.33), residues: 619 helix: -1.01 (0.57), residues: 76 sheet: 0.04 (0.43), residues: 142 loop : 0.05 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 384 HIS 0.006 0.002 HIS A 488 PHE 0.017 0.002 PHE A 594 TYR 0.012 0.001 TYR B 414 ARG 0.003 0.001 ARG B 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00942 ( 4) link_NAG-ASN : angle 3.22116 ( 12) link_BETA1-4 : bond 0.00651 ( 1) link_BETA1-4 : angle 0.89906 ( 3) hydrogen bonds : bond 0.04323 ( 137) hydrogen bonds : angle 5.94619 ( 351) SS BOND : bond 0.00478 ( 19) SS BOND : angle 1.47794 ( 38) covalent geometry : bond 0.00389 ( 4841) covalent geometry : angle 0.59053 ( 6608) *********************** 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 71 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.484 Fit side-chains REVERT: A 486 LYS cc_start: 0.8692 (mttt) cc_final: 0.8291 (mtpp) REVERT: B 147 ARG cc_start: 0.7500 (mmm160) cc_final: 0.7164 (mmm160) REVERT: B 395 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.6966 (tp30) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 0.9581 time to fit residues: 67.5007 Evaluate side-chains 62 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.179075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.151834 restraints weight = 4734.235| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.88 r_work: 0.3580 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4865 Z= 0.147 Angle : 0.583 10.488 6661 Z= 0.302 Chirality : 0.047 0.235 728 Planarity : 0.005 0.041 853 Dihedral : 4.645 34.123 778 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.42 % Favored : 97.42 % Rotamer: Outliers : 2.79 % Allowed : 11.40 % Favored : 85.81 % 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: -0.28 (0.33), residues: 619 helix: -0.91 (0.59), residues: 76 sheet: -0.09 (0.42), residues: 142 loop : 0.02 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 384 HIS 0.005 0.002 HIS A 488 PHE 0.016 0.002 PHE A 594 TYR 0.009 0.001 TYR B 414 ARG 0.005 0.001 ARG A 587 Details of bonding type rmsd link_NAG-ASN : bond 0.01077 ( 4) link_NAG-ASN : angle 3.98277 ( 12) link_BETA1-4 : bond 0.00458 ( 1) link_BETA1-4 : angle 0.89979 ( 3) hydrogen bonds : bond 0.04006 ( 137) hydrogen bonds : angle 5.77480 ( 351) SS BOND : bond 0.00484 ( 19) SS BOND : angle 1.15776 ( 38) covalent geometry : bond 0.00345 ( 4841) covalent geometry : angle 0.55308 ( 6608) *********************** 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 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: 0.8699 (mttt) cc_final: 0.8287 (mtpp) REVERT: A 544 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7779 (pt0) REVERT: B 227 HIS cc_start: 0.8323 (OUTLIER) cc_final: 0.7615 (m90) REVERT: B 395 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.6887 (tp30) REVERT: B 424 MET cc_start: 0.8750 (mtt) cc_final: 0.8486 (mtt) outliers start: 12 outliers final: 5 residues processed: 69 average time/residue: 0.9720 time to fit residues: 70.5097 Evaluate side-chains 68 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 GLU 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 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: 0.5980 chunk 29 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.172920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140633 restraints weight = 4675.257| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.09 r_work: 0.3499 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4865 Z= 0.161 Angle : 0.592 10.647 6661 Z= 0.305 Chirality : 0.048 0.330 728 Planarity : 0.005 0.043 853 Dihedral : 4.595 35.469 778 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.33 % Allowed : 12.09 % Favored : 85.58 % 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 (0.33), residues: 619 helix: -0.94 (0.59), residues: 77 sheet: -0.18 (0.43), residues: 142 loop : 0.05 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 306 HIS 0.005 0.002 HIS A 488 PHE 0.015 0.002 PHE A 594 TYR 0.010 0.001 TYR B 414 ARG 0.002 0.000 ARG A 587 Details of bonding type rmsd link_NAG-ASN : bond 0.01108 ( 4) link_NAG-ASN : angle 3.99652 ( 12) link_BETA1-4 : bond 0.00475 ( 1) link_BETA1-4 : angle 0.84145 ( 3) hydrogen bonds : bond 0.04017 ( 137) hydrogen bonds : angle 5.80906 ( 351) SS BOND : bond 0.00497 ( 19) SS BOND : angle 1.20607 ( 38) covalent geometry : bond 0.00380 ( 4841) covalent geometry : angle 0.56132 ( 6608) *********************** 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 72 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 486 LYS cc_start: 0.8712 (mttt) cc_final: 0.8223 (mtpp) REVERT: B 395 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.6982 (tp30) REVERT: B 424 MET cc_start: 0.8612 (mtt) cc_final: 0.8352 (mtt) outliers start: 10 outliers final: 5 residues processed: 67 average time/residue: 0.9347 time to fit residues: 65.8924 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 289 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: 0.9990 chunk 17 optimal weight: 0.0670 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 0.0470 chunk 42 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 60 optimal weight: 0.0370 overall best weight: 0.2894 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.177399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.145355 restraints weight = 4632.269| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.08 r_work: 0.3553 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4865 Z= 0.096 Angle : 0.515 11.155 6661 Z= 0.266 Chirality : 0.046 0.320 728 Planarity : 0.004 0.043 853 Dihedral : 4.217 35.885 778 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.33 % Allowed : 13.02 % Favored : 84.65 % 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 (0.34), residues: 619 helix: -0.78 (0.61), residues: 77 sheet: -0.16 (0.43), residues: 142 loop : 0.15 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 306 HIS 0.003 0.001 HIS B 274 PHE 0.013 0.001 PHE A 594 TYR 0.007 0.001 TYR A 427 ARG 0.003 0.000 ARG A 587 Details of bonding type rmsd link_NAG-ASN : bond 0.01020 ( 4) link_NAG-ASN : angle 4.04444 ( 12) link_BETA1-4 : bond 0.00426 ( 1) link_BETA1-4 : angle 0.83259 ( 3) hydrogen bonds : bond 0.03327 ( 137) hydrogen bonds : angle 5.38305 ( 351) SS BOND : bond 0.00240 ( 19) SS BOND : angle 0.94374 ( 38) covalent geometry : bond 0.00215 ( 4841) covalent geometry : angle 0.48161 ( 6608) *********************** 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 74 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8382 (mp) cc_final: 0.8170 (mp) REVERT: A 486 LYS cc_start: 0.8637 (mttt) cc_final: 0.8159 (mtpp) REVERT: B 227 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7380 (m90) REVERT: B 395 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.6763 (tp30) outliers start: 10 outliers final: 3 residues processed: 68 average time/residue: 0.8380 time to fit residues: 60.2520 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 395 GLU 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: 0.7980 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 42 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.175713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.143382 restraints weight = 4579.225| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.07 r_work: 0.3533 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4865 Z= 0.122 Angle : 0.545 10.985 6661 Z= 0.281 Chirality : 0.047 0.312 728 Planarity : 0.004 0.044 853 Dihedral : 4.286 36.507 778 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.02 % Allowed : 12.56 % 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: -0.18 (0.34), residues: 619 helix: -0.83 (0.61), residues: 77 sheet: -0.13 (0.43), residues: 142 loop : 0.15 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 306 HIS 0.004 0.001 HIS A 488 PHE 0.013 0.001 PHE A 594 TYR 0.008 0.001 TYR B 414 ARG 0.003 0.000 ARG A 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00994 ( 4) link_NAG-ASN : angle 3.97415 ( 12) link_BETA1-4 : bond 0.00488 ( 1) link_BETA1-4 : angle 0.86583 ( 3) hydrogen bonds : bond 0.03582 ( 137) hydrogen bonds : angle 5.44924 ( 351) SS BOND : bond 0.00425 ( 19) SS BOND : angle 1.01955 ( 38) covalent geometry : bond 0.00283 ( 4841) covalent geometry : angle 0.51445 ( 6608) *********************** 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 72 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8157 (mp) REVERT: A 486 LYS cc_start: 0.8635 (mttt) cc_final: 0.8152 (mtpp) REVERT: A 589 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.6147 (m-40) REVERT: B 227 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7387 (m90) REVERT: B 395 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.6862 (tp30) REVERT: B 424 MET cc_start: 0.8603 (mtt) cc_final: 0.8248 (mtt) outliers start: 13 outliers final: 5 residues processed: 66 average time/residue: 0.8793 time to fit residues: 61.1744 Evaluate side-chains 68 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 583 VAL 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 395 GLU 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: 1.9990 chunk 30 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.173818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.141139 restraints weight = 4589.954| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.09 r_work: 0.3506 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4865 Z= 0.153 Angle : 0.574 11.029 6661 Z= 0.296 Chirality : 0.048 0.316 728 Planarity : 0.005 0.044 853 Dihedral : 4.418 36.506 778 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.56 % Allowed : 13.26 % Favored : 84.19 % 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: -0.23 (0.34), residues: 619 helix: -0.94 (0.59), residues: 77 sheet: -0.14 (0.43), residues: 142 loop : 0.11 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 306 HIS 0.004 0.002 HIS A 488 PHE 0.014 0.001 PHE A 594 TYR 0.009 0.001 TYR B 414 ARG 0.004 0.000 ARG A 587 Details of bonding type rmsd link_NAG-ASN : bond 0.01000 ( 4) link_NAG-ASN : angle 3.96018 ( 12) link_BETA1-4 : bond 0.00498 ( 1) link_BETA1-4 : angle 0.85663 ( 3) hydrogen bonds : bond 0.03833 ( 137) hydrogen bonds : angle 5.65165 ( 351) SS BOND : bond 0.00482 ( 19) SS BOND : angle 1.24409 ( 38) covalent geometry : bond 0.00363 ( 4841) covalent geometry : angle 0.54220 ( 6608) *********************** 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 68 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8227 (mp) REVERT: A 486 LYS cc_start: 0.8698 (mttt) cc_final: 0.8211 (mtpp) REVERT: A 589 ASN cc_start: 0.7231 (OUTLIER) cc_final: 0.6157 (m-40) REVERT: B 227 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7442 (m90) REVERT: B 395 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.6972 (tp30) outliers start: 11 outliers final: 6 residues processed: 63 average time/residue: 0.8776 time to fit residues: 58.4917 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 583 VAL 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 395 GLU 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: 0.9980 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.172593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.143625 restraints weight = 4611.363| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.95 r_work: 0.3501 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4865 Z= 0.171 Angle : 0.592 10.993 6661 Z= 0.306 Chirality : 0.048 0.314 728 Planarity : 0.005 0.044 853 Dihedral : 4.534 36.765 778 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.26 % Allowed : 12.79 % Favored : 83.95 % 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: -0.28 (0.34), residues: 619 helix: -1.03 (0.58), residues: 77 sheet: -0.15 (0.43), residues: 142 loop : 0.09 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 306 HIS 0.005 0.002 HIS A 488 PHE 0.014 0.002 PHE A 594 TYR 0.010 0.001 TYR B 414 ARG 0.003 0.000 ARG A 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00983 ( 4) link_NAG-ASN : angle 3.94336 ( 12) link_BETA1-4 : bond 0.00514 ( 1) link_BETA1-4 : angle 0.85910 ( 3) hydrogen bonds : bond 0.03973 ( 137) hydrogen bonds : angle 5.74716 ( 351) SS BOND : bond 0.00512 ( 19) SS BOND : angle 1.34474 ( 38) covalent geometry : bond 0.00409 ( 4841) covalent geometry : angle 0.56025 ( 6608) *********************** 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 70 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 403 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7139 (mt) REVERT: A 486 LYS cc_start: 0.8704 (mttt) cc_final: 0.8265 (mtpt) REVERT: A 589 ASN cc_start: 0.7301 (OUTLIER) cc_final: 0.6281 (m-40) REVERT: B 227 HIS cc_start: 0.8182 (OUTLIER) cc_final: 0.7524 (m90) REVERT: B 395 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.6991 (tp30) outliers start: 14 outliers final: 6 residues processed: 62 average time/residue: 0.9078 time to fit residues: 59.5914 Evaluate side-chains 67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 583 VAL 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 395 GLU 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: 0.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.172931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140439 restraints weight = 4635.719| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.08 r_work: 0.3495 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4865 Z= 0.154 Angle : 0.587 11.038 6661 Z= 0.300 Chirality : 0.048 0.312 728 Planarity : 0.005 0.044 853 Dihedral : 4.483 36.592 778 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.56 % Allowed : 13.72 % 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: -0.33 (0.34), residues: 619 helix: -1.06 (0.58), residues: 77 sheet: -0.26 (0.43), residues: 144 loop : 0.09 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 306 HIS 0.005 0.001 HIS A 488 PHE 0.012 0.001 PHE A 594 TYR 0.009 0.001 TYR B 414 ARG 0.004 0.000 ARG A 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00980 ( 4) link_NAG-ASN : angle 3.94802 ( 12) link_BETA1-4 : bond 0.00502 ( 1) link_BETA1-4 : angle 0.85866 ( 3) hydrogen bonds : bond 0.03846 ( 137) hydrogen bonds : angle 5.75503 ( 351) SS BOND : bond 0.00486 ( 19) SS BOND : angle 1.23721 ( 38) covalent geometry : bond 0.00367 ( 4841) covalent geometry : angle 0.55665 ( 6608) ********************** 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 67 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 403 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7113 (mt) REVERT: A 486 LYS cc_start: 0.8754 (mttt) cc_final: 0.8228 (mtpp) REVERT: A 589 ASN cc_start: 0.7348 (OUTLIER) cc_final: 0.6294 (m-40) REVERT: B 227 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7556 (m90) REVERT: B 395 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7006 (tp30) outliers start: 11 outliers final: 6 residues processed: 62 average time/residue: 0.9929 time to fit residues: 64.8499 Evaluate side-chains 64 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 583 VAL 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 395 GLU 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: 0.5980 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.171935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139096 restraints weight = 4684.939| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.11 r_work: 0.3482 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4865 Z= 0.175 Angle : 0.605 11.019 6661 Z= 0.310 Chirality : 0.049 0.310 728 Planarity : 0.005 0.044 853 Dihedral : 4.594 36.507 778 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.56 % Allowed : 14.19 % 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: -0.36 (0.34), residues: 619 helix: -1.16 (0.57), residues: 77 sheet: -0.20 (0.43), residues: 142 loop : 0.05 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 306 HIS 0.005 0.002 HIS A 488 PHE 0.011 0.002 PHE A 594 TYR 0.011 0.001 TYR B 414 ARG 0.005 0.001 ARG B 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00974 ( 4) link_NAG-ASN : angle 3.93704 ( 12) link_BETA1-4 : bond 0.00521 ( 1) link_BETA1-4 : angle 0.87982 ( 3) hydrogen bonds : bond 0.04007 ( 137) hydrogen bonds : angle 5.84177 ( 351) SS BOND : bond 0.00521 ( 19) SS BOND : angle 1.31270 ( 38) covalent geometry : bond 0.00419 ( 4841) covalent geometry : angle 0.57457 ( 6608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3721.73 seconds wall clock time: 64 minutes 49.56 seconds (3889.56 seconds total)