Starting phenix.real_space_refine on Wed Sep 17 05:04:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgt_43224/09_2025/8vgt_43224.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgt_43224/09_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_43224/09_2025/8vgt_43224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgt_43224/09_2025/8vgt_43224.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgt_43224/09_2025/8vgt_43224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgt_43224/09_2025/8vgt_43224.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.126 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 8, 'ASN:plan1': 7, 'ARG:plan': 2, 'GLU:plan': 1} 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: {'ASN:plan1': 5, 'ASP:plan': 9, 'HIS:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 3, 'TYR:plan': 1} 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: 1.52, per 1000 atoms: 0.32 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: 0.45 Conformation dependent library (CDL) restraints added in 196.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.21 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: 1.02 Time building geometry restraints manager: 0.62 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: 2.240 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.430 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.180 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (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 ARG 0.005 0.001 ARG B 147 TYR 0.035 0.004 TYR B 485 PHE 0.021 0.004 PHE A 450 TRP 0.026 0.005 TRP B 267 HIS 0.008 0.002 HIS A 512 Details of bonding type rmsd covalent geometry : bond 0.01085 ( 4841) covalent geometry : angle 1.29917 ( 6608) SS BOND : bond 0.03699 ( 19) SS BOND : angle 4.88900 ( 38) hydrogen bonds : bond 0.17926 ( 137) hydrogen bonds : angle 8.82028 ( 351) link_BETA1-4 : bond 0.04592 ( 1) link_BETA1-4 : angle 2.32085 ( 3) link_NAG-ASN : bond 0.05612 ( 4) link_NAG-ASN : angle 1.85987 ( 12) *********************** 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 : 0.138 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: 0.5449 time to fit residues: 57.1172 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 : 0.179 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.0170 chunk 25 optimal weight: 3.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.184942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.157890 restraints weight = 4725.274| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.90 r_work: 0.3629 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4865 Z= 0.135 Angle : 0.612 6.542 6661 Z= 0.321 Chirality : 0.049 0.317 728 Planarity : 0.005 0.037 853 Dihedral : 5.556 56.704 782 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.94 % Favored : 97.90 % Rotamer: Outliers : 1.16 % Allowed : 11.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.32), residues: 619 helix: -1.22 (0.56), residues: 76 sheet: 0.72 (0.47), residues: 113 loop : -0.16 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 587 TYR 0.010 0.001 TYR A 427 PHE 0.016 0.002 PHE A 594 TRP 0.016 0.001 TRP B 384 HIS 0.006 0.002 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 4841) covalent geometry : angle 0.60108 ( 6608) SS BOND : bond 0.00416 ( 19) SS BOND : angle 1.15385 ( 38) hydrogen bonds : bond 0.04437 ( 137) hydrogen bonds : angle 6.12163 ( 351) link_BETA1-4 : bond 0.00449 ( 1) link_BETA1-4 : angle 1.05740 ( 3) link_NAG-ASN : bond 0.01057 ( 4) link_NAG-ASN : angle 2.04378 ( 12) *********************** 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: 5 poor density : 65 time to evaluate : 0.184 Fit side-chains REVERT: A 334 ASN cc_start: 0.7714 (m110) cc_final: 0.7174 (m-40) REVERT: A 486 LYS cc_start: 0.8522 (mttt) cc_final: 0.8117 (mtpp) REVERT: A 544 GLU cc_start: 0.8362 (pt0) cc_final: 0.8038 (pt0) REVERT: B 147 ARG cc_start: 0.7452 (mmm160) cc_final: 0.6977 (mmm160) REVERT: B 395 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.6860 (tp30) outliers start: 5 outliers final: 2 residues processed: 68 average time/residue: 0.4956 time to fit residues: 35.3069 Evaluate side-chains 58 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.142 ------------------------------------------------------------------------------- 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 48 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 B 343 ASN B 398 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.176824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.149395 restraints weight = 4745.807| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.88 r_work: 0.3542 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4865 Z= 0.216 Angle : 0.664 7.664 6661 Z= 0.345 Chirality : 0.051 0.309 728 Planarity : 0.005 0.040 853 Dihedral : 4.835 32.340 778 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.75 % Favored : 97.09 % Rotamer: Outliers : 2.56 % Allowed : 12.33 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.32), residues: 619 helix: -1.19 (0.56), residues: 76 sheet: -0.05 (0.42), residues: 142 loop : -0.00 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 587 TYR 0.014 0.002 TYR B 414 PHE 0.018 0.002 PHE A 594 TRP 0.016 0.002 TRP B 384 HIS 0.008 0.002 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 4841) covalent geometry : angle 0.64314 ( 6608) SS BOND : bond 0.00936 ( 19) SS BOND : angle 1.57100 ( 38) hydrogen bonds : bond 0.04684 ( 137) hydrogen bonds : angle 6.18839 ( 351) link_BETA1-4 : bond 0.00655 ( 1) link_BETA1-4 : angle 0.95023 ( 3) link_NAG-ASN : bond 0.01042 ( 4) link_NAG-ASN : angle 3.00946 ( 12) *********************** 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 70 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.176 Fit side-chains REVERT: A 486 LYS cc_start: 0.8684 (mttt) cc_final: 0.8260 (mtpp) REVERT: B 147 ARG cc_start: 0.7521 (mmm160) cc_final: 0.7183 (mmm160) REVERT: B 388 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7047 (pt0) REVERT: B 395 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7014 (tp30) outliers start: 11 outliers final: 5 residues processed: 66 average time/residue: 0.5293 time to fit residues: 36.4925 Evaluate side-chains 62 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 46 optimal weight: 0.8980 chunk 57 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 0.0670 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.180544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.153310 restraints weight = 4689.435| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.88 r_work: 0.3598 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4865 Z= 0.120 Angle : 0.561 10.636 6661 Z= 0.291 Chirality : 0.047 0.330 728 Planarity : 0.005 0.042 853 Dihedral : 4.539 34.119 778 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.42 % Favored : 97.42 % Rotamer: Outliers : 2.79 % Allowed : 12.09 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.33), residues: 619 helix: -0.93 (0.59), residues: 76 sheet: -0.04 (0.43), residues: 142 loop : 0.10 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 587 TYR 0.008 0.001 TYR B 414 PHE 0.015 0.001 PHE A 594 TRP 0.014 0.001 TRP B 384 HIS 0.004 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4841) covalent geometry : angle 0.52925 ( 6608) SS BOND : bond 0.00418 ( 19) SS BOND : angle 1.11377 ( 38) hydrogen bonds : bond 0.03744 ( 137) hydrogen bonds : angle 5.67445 ( 351) link_BETA1-4 : bond 0.00507 ( 1) link_BETA1-4 : angle 0.86204 ( 3) link_NAG-ASN : bond 0.01163 ( 4) link_NAG-ASN : angle 4.01883 ( 12) *********************** 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 : 0.127 Fit side-chains revert: symmetry clash REVERT: A 486 LYS cc_start: 0.8688 (mttt) cc_final: 0.8265 (mtpp) REVERT: B 388 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7105 (pt0) REVERT: B 395 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.6778 (tp30) REVERT: B 424 MET cc_start: 0.8843 (mtt) cc_final: 0.8349 (mtt) outliers start: 12 outliers final: 4 residues processed: 68 average time/residue: 0.4955 time to fit residues: 35.2714 Evaluate side-chains 66 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 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 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 47 optimal weight: 0.0670 chunk 38 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.175452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.143431 restraints weight = 4621.027| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.07 r_work: 0.3533 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4865 Z= 0.124 Angle : 0.551 10.437 6661 Z= 0.284 Chirality : 0.047 0.319 728 Planarity : 0.004 0.044 853 Dihedral : 4.366 35.305 778 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.34), residues: 619 helix: -0.88 (0.59), residues: 77 sheet: -0.13 (0.42), residues: 142 loop : 0.12 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 587 TYR 0.008 0.001 TYR B 414 PHE 0.014 0.001 PHE A 594 TRP 0.015 0.001 TRP B 306 HIS 0.004 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4841) covalent geometry : angle 0.51959 ( 6608) SS BOND : bond 0.00426 ( 19) SS BOND : angle 1.09904 ( 38) hydrogen bonds : bond 0.03672 ( 137) hydrogen bonds : angle 5.57017 ( 351) link_BETA1-4 : bond 0.00549 ( 1) link_BETA1-4 : angle 0.86295 ( 3) link_NAG-ASN : bond 0.01094 ( 4) link_NAG-ASN : angle 3.96933 ( 12) *********************** 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 77 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 486 LYS cc_start: 0.8672 (mttt) cc_final: 0.8171 (mtpp) REVERT: B 227 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7402 (m90) REVERT: B 388 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6969 (pt0) REVERT: B 395 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.6877 (tp30) REVERT: B 424 MET cc_start: 0.8626 (mtt) cc_final: 0.8175 (mtt) outliers start: 12 outliers final: 6 residues processed: 69 average time/residue: 0.5029 time to fit residues: 36.2723 Evaluate side-chains 70 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 437 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 59 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 0.0570 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.174322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.141739 restraints weight = 4716.496| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.11 r_work: 0.3510 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4865 Z= 0.138 Angle : 0.555 10.892 6661 Z= 0.287 Chirality : 0.047 0.325 728 Planarity : 0.004 0.044 853 Dihedral : 4.384 36.476 778 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.79 % Allowed : 12.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.34), residues: 619 helix: -0.90 (0.60), residues: 77 sheet: -0.16 (0.43), residues: 142 loop : 0.13 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 587 TYR 0.009 0.001 TYR B 414 PHE 0.014 0.001 PHE A 594 TRP 0.018 0.001 TRP B 306 HIS 0.004 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4841) covalent geometry : angle 0.52370 ( 6608) SS BOND : bond 0.00463 ( 19) SS BOND : angle 1.09382 ( 38) hydrogen bonds : bond 0.03736 ( 137) hydrogen bonds : angle 5.59272 ( 351) link_BETA1-4 : bond 0.00478 ( 1) link_BETA1-4 : angle 0.85179 ( 3) link_NAG-ASN : bond 0.01059 ( 4) link_NAG-ASN : angle 3.99753 ( 12) *********************** 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 72 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8410 (mp) cc_final: 0.8201 (mp) REVERT: A 486 LYS cc_start: 0.8679 (mttt) cc_final: 0.8199 (mtpp) REVERT: A 589 ASN cc_start: 0.7514 (OUTLIER) cc_final: 0.6479 (m-40) REVERT: B 227 HIS cc_start: 0.8151 (OUTLIER) cc_final: 0.7477 (m90) REVERT: B 388 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6996 (pt0) REVERT: B 395 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.6916 (tp30) outliers start: 12 outliers final: 6 residues processed: 65 average time/residue: 0.4301 time to fit residues: 29.4551 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 : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 309 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 0.5980 chunk 1 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.174627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.142259 restraints weight = 4647.171| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.09 r_work: 0.3518 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3286 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= 0.133 Angle : 0.561 10.757 6661 Z= 0.288 Chirality : 0.047 0.315 728 Planarity : 0.004 0.044 853 Dihedral : 4.356 37.053 778 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.02 % Allowed : 13.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.34), residues: 619 helix: -0.90 (0.60), residues: 77 sheet: -0.13 (0.43), residues: 142 loop : 0.14 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 165 TYR 0.008 0.001 TYR B 414 PHE 0.013 0.001 PHE A 594 TRP 0.020 0.001 TRP B 306 HIS 0.004 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 4841) covalent geometry : angle 0.53171 ( 6608) SS BOND : bond 0.00470 ( 19) SS BOND : angle 1.06484 ( 38) hydrogen bonds : bond 0.03662 ( 137) hydrogen bonds : angle 5.55328 ( 351) link_BETA1-4 : bond 0.00462 ( 1) link_BETA1-4 : angle 0.84108 ( 3) link_NAG-ASN : bond 0.01008 ( 4) link_NAG-ASN : angle 3.93227 ( 12) *********************** 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 76 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 486 LYS cc_start: 0.8677 (mttt) cc_final: 0.8188 (mtpp) REVERT: A 589 ASN cc_start: 0.7281 (OUTLIER) cc_final: 0.6189 (m-40) REVERT: B 227 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7458 (m90) REVERT: B 388 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6959 (pt0) REVERT: B 395 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.6900 (tp30) REVERT: B 424 MET cc_start: 0.8645 (mtt) cc_final: 0.8025 (mtt) outliers start: 13 outliers final: 6 residues processed: 69 average time/residue: 0.5193 time to fit residues: 37.5328 Evaluate side-chains 72 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 309 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 49 optimal weight: 0.1980 chunk 58 optimal weight: 0.1980 chunk 18 optimal weight: 0.4980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.177340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.145007 restraints weight = 4659.260| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.10 r_work: 0.3546 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4865 Z= 0.100 Angle : 0.519 10.834 6661 Z= 0.267 Chirality : 0.046 0.317 728 Planarity : 0.004 0.046 853 Dihedral : 4.109 37.035 778 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.79 % Allowed : 14.19 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.34), residues: 619 helix: -0.82 (0.61), residues: 77 sheet: -0.11 (0.43), residues: 142 loop : 0.17 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 186 TYR 0.011 0.001 TYR B 226 PHE 0.012 0.001 PHE A 594 TRP 0.018 0.001 TRP B 306 HIS 0.003 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 4841) covalent geometry : angle 0.48808 ( 6608) SS BOND : bond 0.00354 ( 19) SS BOND : angle 0.93992 ( 38) hydrogen bonds : bond 0.03281 ( 137) hydrogen bonds : angle 5.33320 ( 351) link_BETA1-4 : bond 0.00442 ( 1) link_BETA1-4 : angle 0.85179 ( 3) link_NAG-ASN : bond 0.00998 ( 4) link_NAG-ASN : angle 3.92363 ( 12) *********************** 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 74 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 486 LYS cc_start: 0.8661 (mttt) cc_final: 0.8189 (mtpp) REVERT: A 589 ASN cc_start: 0.7318 (OUTLIER) cc_final: 0.6319 (m-40) REVERT: B 227 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7344 (m90) REVERT: B 388 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6933 (pt0) REVERT: B 395 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.6836 (tp30) REVERT: B 424 MET cc_start: 0.8633 (mtt) cc_final: 0.8127 (mtt) outliers start: 12 outliers final: 4 residues processed: 66 average time/residue: 0.4619 time to fit residues: 32.0637 Evaluate side-chains 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 388 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 55 optimal weight: 0.0770 chunk 30 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 7 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.176453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.147618 restraints weight = 4641.673| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.94 r_work: 0.3540 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3412 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= 0.110 Angle : 0.529 10.596 6661 Z= 0.272 Chirality : 0.047 0.312 728 Planarity : 0.004 0.044 853 Dihedral : 4.116 37.215 778 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.33 % Allowed : 14.65 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.34), residues: 619 helix: -0.87 (0.61), residues: 77 sheet: -0.08 (0.43), residues: 142 loop : 0.19 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 186 TYR 0.007 0.001 TYR B 414 PHE 0.012 0.001 PHE A 594 TRP 0.024 0.001 TRP B 306 HIS 0.003 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 4841) covalent geometry : angle 0.49958 ( 6608) SS BOND : bond 0.00365 ( 19) SS BOND : angle 0.96990 ( 38) hydrogen bonds : bond 0.03396 ( 137) hydrogen bonds : angle 5.34688 ( 351) link_BETA1-4 : bond 0.00465 ( 1) link_BETA1-4 : angle 0.87002 ( 3) link_NAG-ASN : bond 0.00983 ( 4) link_NAG-ASN : angle 3.85280 ( 12) *********************** 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 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 486 LYS cc_start: 0.8679 (mttt) cc_final: 0.8256 (mtpp) REVERT: A 589 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.6350 (m-40) REVERT: B 227 HIS cc_start: 0.8175 (OUTLIER) cc_final: 0.7370 (m90) REVERT: B 388 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7003 (pt0) REVERT: B 395 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.6870 (tp30) outliers start: 10 outliers final: 5 residues processed: 60 average time/residue: 0.5104 time to fit residues: 32.0105 Evaluate side-chains 62 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 388 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 38 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 53 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.174984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.142508 restraints weight = 4601.681| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.09 r_work: 0.3519 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3438 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= 0.130 Angle : 0.560 10.523 6661 Z= 0.284 Chirality : 0.047 0.315 728 Planarity : 0.004 0.044 853 Dihedral : 4.206 37.331 778 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.56 % Allowed : 14.42 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.34), residues: 619 helix: -0.92 (0.60), residues: 77 sheet: -0.13 (0.43), residues: 142 loop : 0.18 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 186 TYR 0.008 0.001 TYR B 414 PHE 0.012 0.001 PHE A 594 TRP 0.024 0.001 TRP B 306 HIS 0.004 0.001 HIS A 488 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4841) covalent geometry : angle 0.53227 ( 6608) SS BOND : bond 0.00408 ( 19) SS BOND : angle 1.03453 ( 38) hydrogen bonds : bond 0.03546 ( 137) hydrogen bonds : angle 5.51591 ( 351) link_BETA1-4 : bond 0.00466 ( 1) link_BETA1-4 : angle 0.87101 ( 3) link_NAG-ASN : bond 0.00983 ( 4) link_NAG-ASN : angle 3.81198 ( 12) ********************** 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 65 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 388 LEU cc_start: 0.8301 (mp) cc_final: 0.8001 (mp) REVERT: A 486 LYS cc_start: 0.8667 (mttt) cc_final: 0.8212 (mtpp) REVERT: A 589 ASN cc_start: 0.7305 (OUTLIER) cc_final: 0.6264 (m-40) REVERT: B 227 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7380 (m90) REVERT: B 388 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6936 (pt0) REVERT: B 395 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.6922 (tp30) REVERT: B 424 MET cc_start: 0.8595 (mtt) cc_final: 0.8118 (mtt) outliers start: 11 outliers final: 6 residues processed: 60 average time/residue: 0.4676 time to fit residues: 29.5096 Evaluate side-chains 63 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ILE 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 388 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 35 optimal weight: 0.0060 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.0670 chunk 55 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 overall best weight: 0.2934 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.177421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.145166 restraints weight = 4654.737| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.09 r_work: 0.3550 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3475 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= 0.099 Angle : 0.525 10.509 6661 Z= 0.267 Chirality : 0.047 0.316 728 Planarity : 0.004 0.044 853 Dihedral : 4.033 37.284 778 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.33 % Allowed : 14.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.34), residues: 619 helix: -0.84 (0.61), residues: 77 sheet: -0.07 (0.43), residues: 142 loop : 0.22 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 186 TYR 0.007 0.001 TYR B 414 PHE 0.010 0.001 PHE A 594 TRP 0.020 0.001 TRP B 306 HIS 0.004 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 4841) covalent geometry : angle 0.49602 ( 6608) SS BOND : bond 0.00393 ( 19) SS BOND : angle 0.96917 ( 38) hydrogen bonds : bond 0.03277 ( 137) hydrogen bonds : angle 5.31667 ( 351) link_BETA1-4 : bond 0.00459 ( 1) link_BETA1-4 : angle 0.88764 ( 3) link_NAG-ASN : bond 0.00966 ( 4) link_NAG-ASN : angle 3.79207 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1881.00 seconds wall clock time: 32 minutes 41.27 seconds (1961.27 seconds total)