Starting phenix.real_space_refine on Tue Mar 3 19:53:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c8k_30306/03_2026/7c8k_30306.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c8k_30306/03_2026/7c8k_30306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c8k_30306/03_2026/7c8k_30306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c8k_30306/03_2026/7c8k_30306.map" model { file = "/net/cci-nas-00/data/ceres_data/7c8k_30306/03_2026/7c8k_30306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c8k_30306/03_2026/7c8k_30306.cif" } resolution = 3.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4459 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 29 5.16 5 C 3104 2.51 5 N 804 2.21 5 O 915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4853 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4782 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 566} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 5, 'ASP:plan': 5, 'ARG:plan': 3, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "B" 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.29, per 1000 atoms: 0.27 Number of scatterers: 4853 At special positions: 0 Unit cell: (78.5062, 87.45, 79.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 29 16.00 O 915 8.00 N 804 7.00 C 3104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 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 B 1 " - " NAG B 2 " NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 90 " " NAG A 706 " - " ASN A 329 " " NAG B 1 " - " ASN A 546 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 279.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 705 " pdb="ZN ZN A 705 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 705 " - pdb=" NE2 HIS A 374 " 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 3 sheets defined 66.6% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.564A pdb=" N GLU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 82 removed outlier: 3.688A pdb=" N GLN A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.690A pdb=" N LYS A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.573A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 249 removed outlier: 3.639A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.557A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.698A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.772A pdb=" N ASN A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 4.119A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.521A pdb=" N LEU A 503 " --> pdb=" O PRO A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.953A pdb=" N ASN A 508 " --> pdb=" O HIS A 505 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A 509 " --> pdb=" O VAL A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.717A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.705A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.652A pdb=" N ILE A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.562A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 258 hydrogen bonds defined for protein. 753 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: 0.66 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1541 1.34 - 1.46: 1058 1.46 - 1.58: 2340 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 4989 Sorted by residual: bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 NAG A 706 " pdb=" O5 NAG A 706 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.39e+00 ... (remaining 4984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 6659 1.72 - 3.44: 99 3.44 - 5.16: 12 5.16 - 6.88: 2 6.88 - 8.60: 1 Bond angle restraints: 6773 Sorted by residual: angle pdb=" N VAL A 107 " pdb=" CA VAL A 107 " pdb=" C VAL A 107 " ideal model delta sigma weight residual 113.71 109.31 4.40 9.50e-01 1.11e+00 2.15e+01 angle pdb=" N ILE A 544 " pdb=" CA ILE A 544 " pdb=" C ILE A 544 " ideal model delta sigma weight residual 113.22 109.12 4.10 1.23e+00 6.61e-01 1.11e+01 angle pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta sigma weight residual 122.21 130.81 -8.60 2.87e+00 1.21e-01 8.99e+00 angle pdb=" C ILE A 233 " pdb=" N LYS A 234 " pdb=" CA LYS A 234 " ideal model delta sigma weight residual 121.62 125.48 -3.86 1.57e+00 4.06e-01 6.04e+00 angle pdb=" CA VAL A 107 " pdb=" C VAL A 107 " pdb=" N LEU A 108 " ideal model delta sigma weight residual 119.87 116.80 3.07 1.34e+00 5.57e-01 5.24e+00 ... (remaining 6768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 2752 17.16 - 34.33: 211 34.33 - 51.49: 42 51.49 - 68.65: 6 68.65 - 85.81: 10 Dihedral angle restraints: 3021 sinusoidal: 1273 harmonic: 1748 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -124.47 38.47 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CB GLU A 310 " pdb=" CG GLU A 310 " pdb=" CD GLU A 310 " pdb=" OE1 GLU A 310 " ideal model delta sinusoidal sigma weight residual 0.00 -85.81 85.81 1 3.00e+01 1.11e-03 9.89e+00 dihedral pdb=" CB GLU A 208 " pdb=" CG GLU A 208 " pdb=" CD GLU A 208 " pdb=" OE1 GLU A 208 " ideal model delta sinusoidal sigma weight residual 0.00 -83.89 83.89 1 3.00e+01 1.11e-03 9.53e+00 ... (remaining 3018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 719 0.134 - 0.267: 2 0.267 - 0.401: 0 0.401 - 0.535: 0 0.535 - 0.668: 1 Chirality restraints: 722 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-02 2.50e+03 1.12e+03 chirality pdb=" CB VAL A 581 " pdb=" CA VAL A 581 " pdb=" CG1 VAL A 581 " pdb=" CG2 VAL A 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA VAL A 318 " pdb=" N VAL A 318 " pdb=" C VAL A 318 " pdb=" CB VAL A 318 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 719 not shown) Planarity restraints: 865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 582 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 583 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 146 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " 0.016 5.00e-02 4.00e+02 2.44e-02 9.55e-01 pdb=" N PRO A 235 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.014 5.00e-02 4.00e+02 ... (remaining 862 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 38 2.58 - 3.16: 3919 3.16 - 3.74: 7832 3.74 - 4.32: 10681 4.32 - 4.90: 17675 Nonbonded interactions: 40145 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 705 " model vdw 2.001 2.230 nonbonded pdb=" OD1 ASP A 227 " pdb=" OH TYR A 454 " model vdw 2.295 3.040 nonbonded pdb=" OD1 ASP A 543 " pdb=" OG SER A 545 " model vdw 2.298 3.040 nonbonded pdb=" O TRP A 48 " pdb=" OG1 THR A 52 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.303 3.040 ... (remaining 40140 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.910 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.199 4999 Z= 0.193 Angle : 0.588 16.900 6794 Z= 0.308 Chirality : 0.045 0.668 722 Planarity : 0.003 0.041 861 Dihedral : 13.488 85.814 1888 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: -1.52 (0.31), residues: 594 helix: -0.16 (0.26), residues: 353 sheet: None (None), residues: 0 loop : -2.29 (0.33), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 306 TYR 0.005 0.001 TYR A 237 PHE 0.004 0.001 PHE A 400 TRP 0.004 0.000 TRP A 473 HIS 0.001 0.000 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 4989) covalent geometry : angle 0.51474 ( 6773) SS BOND : bond 0.00033 ( 3) SS BOND : angle 0.22212 ( 6) hydrogen bonds : bond 0.12309 ( 258) hydrogen bonds : angle 5.42381 ( 753) metal coordination : bond 0.19918 ( 2) link_BETA1-4 : bond 0.06524 ( 1) link_BETA1-4 : angle 13.51957 ( 3) link_NAG-ASN : bond 0.00174 ( 4) link_NAG-ASN : angle 0.85054 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8357 (m-40) cc_final: 0.8134 (m-40) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.0875 time to fit residues: 10.5562 Evaluate side-chains 51 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.105253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.088110 restraints weight = 10323.519| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.37 r_work: 0.3198 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4999 Z= 0.106 Angle : 0.493 6.419 6794 Z= 0.243 Chirality : 0.040 0.160 722 Planarity : 0.004 0.053 861 Dihedral : 3.933 33.146 751 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.40 % Allowed : 6.80 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 0.08 (0.34), residues: 594 helix: 1.17 (0.28), residues: 353 sheet: -2.66 (1.12), residues: 12 loop : -1.60 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 531 TYR 0.013 0.001 TYR A 243 PHE 0.009 0.001 PHE A 512 TRP 0.005 0.001 TRP A 478 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 4989) covalent geometry : angle 0.49062 ( 6773) SS BOND : bond 0.00294 ( 3) SS BOND : angle 0.35391 ( 6) hydrogen bonds : bond 0.03123 ( 258) hydrogen bonds : angle 3.80294 ( 753) metal coordination : bond 0.00622 ( 2) link_BETA1-4 : bond 0.00710 ( 1) link_BETA1-4 : angle 2.11588 ( 3) link_NAG-ASN : bond 0.00300 ( 4) link_NAG-ASN : angle 0.80854 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8750 (m-40) cc_final: 0.8488 (m-40) REVERT: A 609 ASP cc_start: 0.8267 (p0) cc_final: 0.8049 (p0) outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.0512 time to fit residues: 4.4172 Evaluate side-chains 55 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 10 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.099231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.082389 restraints weight = 9908.699| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.24 r_work: 0.3091 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4999 Z= 0.142 Angle : 0.529 6.563 6794 Z= 0.265 Chirality : 0.041 0.127 722 Planarity : 0.004 0.056 861 Dihedral : 3.505 17.239 751 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.00 % Allowed : 9.60 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 0.59 (0.34), residues: 594 helix: 1.41 (0.28), residues: 368 sheet: -2.38 (1.19), residues: 12 loop : -1.25 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.034 0.002 TYR A 50 PHE 0.018 0.002 PHE A 400 TRP 0.011 0.001 TRP A 473 HIS 0.006 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4989) covalent geometry : angle 0.52482 ( 6773) SS BOND : bond 0.00348 ( 3) SS BOND : angle 0.47170 ( 6) hydrogen bonds : bond 0.03540 ( 258) hydrogen bonds : angle 3.77686 ( 753) metal coordination : bond 0.00124 ( 2) link_BETA1-4 : bond 0.00011 ( 1) link_BETA1-4 : angle 2.15938 ( 3) link_NAG-ASN : bond 0.00191 ( 4) link_NAG-ASN : angle 1.19253 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8946 (m-40) cc_final: 0.8734 (m-40) outliers start: 5 outliers final: 4 residues processed: 54 average time/residue: 0.0482 time to fit residues: 3.9469 Evaluate side-chains 48 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 539 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 0.0170 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.099043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.081611 restraints weight = 10154.286| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.30 r_work: 0.3072 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4999 Z= 0.130 Angle : 0.503 6.249 6794 Z= 0.251 Chirality : 0.040 0.126 722 Planarity : 0.004 0.056 861 Dihedral : 3.436 15.355 751 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.20 % Allowed : 11.40 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 0.90 (0.35), residues: 594 helix: 1.63 (0.28), residues: 368 sheet: -2.61 (1.02), residues: 12 loop : -1.03 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.033 0.001 TYR A 50 PHE 0.013 0.001 PHE A 400 TRP 0.009 0.001 TRP A 478 HIS 0.008 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 4989) covalent geometry : angle 0.49983 ( 6773) SS BOND : bond 0.00341 ( 3) SS BOND : angle 0.50515 ( 6) hydrogen bonds : bond 0.03342 ( 258) hydrogen bonds : angle 3.75624 ( 753) metal coordination : bond 0.00136 ( 2) link_BETA1-4 : bond 0.00107 ( 1) link_BETA1-4 : angle 1.69205 ( 3) link_NAG-ASN : bond 0.00119 ( 4) link_NAG-ASN : angle 1.13219 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8970 (m-40) cc_final: 0.8767 (m-40) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.0473 time to fit residues: 3.8315 Evaluate side-chains 49 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 539 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 53 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.097434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.080037 restraints weight = 10073.487| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.28 r_work: 0.3042 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4999 Z= 0.151 Angle : 0.536 6.276 6794 Z= 0.270 Chirality : 0.041 0.164 722 Planarity : 0.004 0.057 861 Dihedral : 3.583 16.399 751 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.40 % Allowed : 11.80 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 1.04 (0.35), residues: 594 helix: 1.72 (0.28), residues: 368 sheet: -2.49 (1.12), residues: 10 loop : -0.95 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.029 0.001 TYR A 50 PHE 0.016 0.002 PHE A 400 TRP 0.011 0.001 TRP A 478 HIS 0.005 0.001 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4989) covalent geometry : angle 0.53224 ( 6773) SS BOND : bond 0.00406 ( 3) SS BOND : angle 0.72164 ( 6) hydrogen bonds : bond 0.03521 ( 258) hydrogen bonds : angle 3.83037 ( 753) metal coordination : bond 0.00156 ( 2) link_BETA1-4 : bond 0.00200 ( 1) link_BETA1-4 : angle 1.91562 ( 3) link_NAG-ASN : bond 0.00148 ( 4) link_NAG-ASN : angle 1.28283 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 0.0524 time to fit residues: 4.0528 Evaluate side-chains 47 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 539 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 17 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 0.0470 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 0.0000 chunk 12 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 overall best weight: 0.4484 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.100455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.083168 restraints weight = 10173.108| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.32 r_work: 0.3099 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4999 Z= 0.096 Angle : 0.501 7.270 6794 Z= 0.247 Chirality : 0.039 0.180 722 Planarity : 0.004 0.051 861 Dihedral : 3.342 15.971 751 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.60 % Allowed : 12.20 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 1.23 (0.35), residues: 594 helix: 1.87 (0.28), residues: 368 sheet: -2.74 (1.02), residues: 12 loop : -0.84 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.022 0.001 TYR A 50 PHE 0.011 0.001 PHE A 315 TRP 0.012 0.001 TRP A 478 HIS 0.003 0.000 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 4989) covalent geometry : angle 0.49799 ( 6773) SS BOND : bond 0.00274 ( 3) SS BOND : angle 0.45627 ( 6) hydrogen bonds : bond 0.03101 ( 258) hydrogen bonds : angle 3.69160 ( 753) metal coordination : bond 0.00046 ( 2) link_BETA1-4 : bond 0.00350 ( 1) link_BETA1-4 : angle 1.41509 ( 3) link_NAG-ASN : bond 0.00179 ( 4) link_NAG-ASN : angle 1.17197 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8885 (m-40) cc_final: 0.8653 (m-40) outliers start: 3 outliers final: 3 residues processed: 53 average time/residue: 0.0476 time to fit residues: 3.8095 Evaluate side-chains 49 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 364 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 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 = 0.3510 r_free = 0.3510 target = 0.100073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.082578 restraints weight = 10009.164| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.37 r_work: 0.3088 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4999 Z= 0.103 Angle : 0.494 6.972 6794 Z= 0.245 Chirality : 0.039 0.158 722 Planarity : 0.004 0.052 861 Dihedral : 3.293 15.622 751 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.80 % Allowed : 12.00 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 1.34 (0.35), residues: 594 helix: 1.94 (0.28), residues: 368 sheet: -2.61 (1.15), residues: 10 loop : -0.79 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.023 0.001 TYR A 50 PHE 0.008 0.001 PHE A 523 TRP 0.007 0.001 TRP A 165 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 4989) covalent geometry : angle 0.49076 ( 6773) SS BOND : bond 0.00295 ( 3) SS BOND : angle 0.46984 ( 6) hydrogen bonds : bond 0.03177 ( 258) hydrogen bonds : angle 3.69513 ( 753) metal coordination : bond 0.00087 ( 2) link_BETA1-4 : bond 0.00360 ( 1) link_BETA1-4 : angle 1.59452 ( 3) link_NAG-ASN : bond 0.00125 ( 4) link_NAG-ASN : angle 1.19998 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8956 (m-40) cc_final: 0.8714 (m-40) outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.0473 time to fit residues: 3.5795 Evaluate side-chains 47 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 364 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.099635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.082289 restraints weight = 10126.108| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.35 r_work: 0.3081 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4999 Z= 0.107 Angle : 0.495 6.992 6794 Z= 0.244 Chirality : 0.039 0.158 722 Planarity : 0.004 0.052 861 Dihedral : 3.307 16.449 751 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.80 % Allowed : 11.80 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 1.33 (0.35), residues: 594 helix: 1.91 (0.28), residues: 369 sheet: -2.38 (1.18), residues: 10 loop : -0.79 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.022 0.001 TYR A 50 PHE 0.013 0.001 PHE A 315 TRP 0.007 0.001 TRP A 168 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 4989) covalent geometry : angle 0.49144 ( 6773) SS BOND : bond 0.00315 ( 3) SS BOND : angle 0.48810 ( 6) hydrogen bonds : bond 0.03212 ( 258) hydrogen bonds : angle 3.72630 ( 753) metal coordination : bond 0.00130 ( 2) link_BETA1-4 : bond 0.00257 ( 1) link_BETA1-4 : angle 1.57211 ( 3) link_NAG-ASN : bond 0.00108 ( 4) link_NAG-ASN : angle 1.23663 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8992 (m-40) cc_final: 0.8748 (m-40) outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.0450 time to fit residues: 3.3925 Evaluate side-chains 49 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 364 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 48 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 51 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.099796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082537 restraints weight = 9960.323| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.33 r_work: 0.3089 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4999 Z= 0.103 Angle : 0.495 7.200 6794 Z= 0.243 Chirality : 0.039 0.153 722 Planarity : 0.004 0.051 861 Dihedral : 3.278 16.617 751 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.80 % Allowed : 12.40 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 1.41 (0.35), residues: 594 helix: 1.97 (0.28), residues: 368 sheet: -2.38 (1.21), residues: 10 loop : -0.72 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.019 0.001 TYR A 50 PHE 0.014 0.001 PHE A 315 TRP 0.009 0.001 TRP A 168 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 4989) covalent geometry : angle 0.49148 ( 6773) SS BOND : bond 0.00292 ( 3) SS BOND : angle 0.47465 ( 6) hydrogen bonds : bond 0.03161 ( 258) hydrogen bonds : angle 3.71005 ( 753) metal coordination : bond 0.00067 ( 2) link_BETA1-4 : bond 0.00233 ( 1) link_BETA1-4 : angle 1.52211 ( 3) link_NAG-ASN : bond 0.00116 ( 4) link_NAG-ASN : angle 1.23798 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8969 (m-40) cc_final: 0.8725 (m-40) outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.0501 time to fit residues: 3.8081 Evaluate side-chains 49 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 19 optimal weight: 0.0570 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.0170 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.100801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.083505 restraints weight = 9965.319| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.34 r_work: 0.3102 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4999 Z= 0.097 Angle : 0.492 7.292 6794 Z= 0.242 Chirality : 0.039 0.151 722 Planarity : 0.004 0.051 861 Dihedral : 3.219 16.477 751 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.80 % Allowed : 12.80 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 1.45 (0.35), residues: 594 helix: 2.02 (0.28), residues: 366 sheet: -2.47 (1.27), residues: 10 loop : -0.72 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 514 TYR 0.019 0.001 TYR A 50 PHE 0.014 0.001 PHE A 315 TRP 0.007 0.001 TRP A 168 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 4989) covalent geometry : angle 0.48909 ( 6773) SS BOND : bond 0.00248 ( 3) SS BOND : angle 0.44690 ( 6) hydrogen bonds : bond 0.03067 ( 258) hydrogen bonds : angle 3.70226 ( 753) metal coordination : bond 0.00057 ( 2) link_BETA1-4 : bond 0.00174 ( 1) link_BETA1-4 : angle 1.41207 ( 3) link_NAG-ASN : bond 0.00131 ( 4) link_NAG-ASN : angle 1.22791 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8945 (m-40) cc_final: 0.8689 (m-40) outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.0493 time to fit residues: 3.6280 Evaluate side-chains 49 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.100180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.083062 restraints weight = 10025.688| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.32 r_work: 0.3096 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4999 Z= 0.105 Angle : 0.507 7.447 6794 Z= 0.249 Chirality : 0.039 0.151 722 Planarity : 0.004 0.051 861 Dihedral : 3.240 16.618 751 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.80 % Allowed : 13.00 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 are not related in a simple way. whole: 1.41 (0.35), residues: 594 helix: 1.99 (0.28), residues: 369 sheet: -2.42 (1.31), residues: 10 loop : -0.77 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 393 TYR 0.019 0.001 TYR A 50 PHE 0.013 0.001 PHE A 315 TRP 0.007 0.001 TRP A 168 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 4989) covalent geometry : angle 0.50438 ( 6773) SS BOND : bond 0.00281 ( 3) SS BOND : angle 0.45262 ( 6) hydrogen bonds : bond 0.03115 ( 258) hydrogen bonds : angle 3.72658 ( 753) metal coordination : bond 0.00074 ( 2) link_BETA1-4 : bond 0.00238 ( 1) link_BETA1-4 : angle 1.49737 ( 3) link_NAG-ASN : bond 0.00103 ( 4) link_NAG-ASN : angle 1.24283 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1344.80 seconds wall clock time: 23 minutes 39.00 seconds (1419.00 seconds total)