Starting phenix.real_space_refine on Fri Sep 11 07:24:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c8k_30306/09_2026/7c8k_30306.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c8k_30306/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7c8k_30306/09_2026/7c8k_30306.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c8k_30306/09_2026/7c8k_30306.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c8k_30306/09_2026/7c8k_30306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c8k_30306/09_2026/7c8k_30306.map" model { file = "/net/cci-nas-00/data/ceres_data/7c8k_30306/09_2026/7c8k_30306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c8k_30306/09_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-2.2.1-6174/lib/python3.11/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 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 chiralities: 3 Time building chain proxies: 1.25, per 1000 atoms: 0.26 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: 0.38 Conformation dependent library (CDL) restraints added in 144.0 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: 0.13 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: 0.71 Time building geometry restraints manager: 0.52 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: 2655 17.16 - 34.33: 209 34.33 - 51.49: 36 51.49 - 68.65: 6 68.65 - 85.81: 10 Dihedral angle restraints: 2916 sinusoidal: 1168 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 2913 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.700 Find NCS groups from input model: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 : 13.618 85.814 1783 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/Z covalent geometry : bond 0.00242 / 0.13 ( 4989) covalent geometry : angle 0.51474 / 0.29 ( 6773) SS BOND : bond 0.00033 / 0.02 ( 3) SS BOND : angle 0.22212 / 0.11 ( 6) hydrogen bonds : bond 0.12309 / 8.01 ( 258) hydrogen bonds : angle 5.42381 / 4.11 ( 753) metal coordination : bond 0.19918 / 10.00 ( 2) link_BETA1-4 : bond 0.06524 / 3.43 ( 1) link_BETA1-4 : angle 13.51957 / 7.54 ( 3) link_NAG-ASN : bond 0.00174 / 0.09 ( 4) link_NAG-ASN : angle 0.85054 / 0.47 ( 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 : 0.186 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: 0.0857 time to fit residues: 10.3669 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 : 0.190 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.105235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.088220 restraints weight = 10322.657| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.33 r_work: 0.3200 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4999 Z= 0.106 Angle : 0.494 6.596 6794 Z= 0.242 Chirality : 0.040 0.154 722 Planarity : 0.004 0.052 861 Dihedral : 2.964 12.648 646 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.40 % Allowed : 6.60 % Favored : 93.00 % 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: 0.10 (0.34), residues: 594 helix: 1.19 (0.28), residues: 353 sheet: -2.66 (1.11), residues: 12 loop : -1.61 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 531 TYR 0.012 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/Z covalent geometry : bond 0.00238 / 0.11 ( 4989) covalent geometry : angle 0.49192 / 0.24 ( 6773) SS BOND : bond 0.00298 / 0.15 ( 3) SS BOND : angle 0.35816 / 0.19 ( 6) hydrogen bonds : bond 0.03078 / 2.05 ( 258) hydrogen bonds : angle 3.79433 / 2.85 ( 753) metal coordination : bond 0.00477 / 0.25 ( 2) link_BETA1-4 : bond 0.00255 / 0.13 ( 1) link_BETA1-4 : angle 1.71682 / 0.89 ( 3) link_NAG-ASN : bond 0.00174 / 0.09 ( 4) link_NAG-ASN : angle 0.83093 / 0.45 ( 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 59 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8682 (m-40) cc_final: 0.8431 (m-40) REVERT: A 609 ASP cc_start: 0.8173 (p0) cc_final: 0.7940 (p0) outliers start: 2 outliers final: 1 residues processed: 58 average time/residue: 0.0503 time to fit residues: 4.3187 Evaluate side-chains 56 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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: 2.9990 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.082557 restraints weight = 9956.721| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.14 r_work: 0.3095 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4999 Z= 0.160 Angle : 0.538 6.745 6794 Z= 0.269 Chirality : 0.041 0.129 722 Planarity : 0.004 0.056 861 Dihedral : 3.428 15.646 646 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.00 % Allowed : 10.20 % Favored : 88.80 % 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: 0.58 (0.34), residues: 594 helix: 1.40 (0.28), residues: 368 sheet: -2.26 (1.21), residues: 12 loop : -1.26 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 514 TYR 0.037 0.002 TYR A 50 PHE 0.021 0.002 PHE A 400 TRP 0.011 0.001 TRP A 473 HIS 0.007 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 4989) covalent geometry : angle 0.53479 / 0.27 ( 6773) SS BOND : bond 0.00350 / 0.17 ( 3) SS BOND : angle 0.48216 / 0.28 ( 6) hydrogen bonds : bond 0.03558 / 2.41 ( 258) hydrogen bonds : angle 3.80025 / 2.84 ( 753) metal coordination : bond 0.00120 / 0.06 ( 2) link_BETA1-4 : bond 0.00212 / 0.11 ( 1) link_BETA1-4 : angle 2.08818 / 1.06 ( 3) link_NAG-ASN : bond 0.00139 / 0.07 ( 4) link_NAG-ASN : angle 1.24244 / 0.68 ( 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 58 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.0510 time to fit residues: 4.3320 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 : 0.170 ------------------------------------------------------------------------------- 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: 7.9990 chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 0.0970 chunk 55 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.100558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.083236 restraints weight = 10109.669| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.29 r_work: 0.3101 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 4999 Z= 0.105 Angle : 0.487 6.296 6794 Z= 0.242 Chirality : 0.039 0.131 722 Planarity : 0.004 0.054 861 Dihedral : 3.328 14.806 646 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.80 % Allowed : 11.00 % Favored : 88.20 % 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: 0.90 (0.35), residues: 594 helix: 1.65 (0.28), residues: 367 sheet: -2.73 (1.00), residues: 12 loop : -1.07 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.028 0.001 TYR A 50 PHE 0.009 0.001 PHE A 400 TRP 0.008 0.001 TRP A 478 HIS 0.007 0.001 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 4989) covalent geometry : angle 0.48502 / 0.24 ( 6773) SS BOND : bond 0.00306 / 0.15 ( 3) SS BOND : angle 0.45788 / 0.27 ( 6) hydrogen bonds : bond 0.03155 / 2.15 ( 258) hydrogen bonds : angle 3.68448 / 2.75 ( 753) metal coordination : bond 0.00094 / 0.05 ( 2) link_BETA1-4 : bond 0.00375 / 0.20 ( 1) link_BETA1-4 : angle 1.36886 / 0.70 ( 3) link_NAG-ASN : bond 0.00142 / 0.07 ( 4) link_NAG-ASN : angle 1.02624 / 0.56 ( 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 56 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 55 average time/residue: 0.0428 time to fit residues: 3.4978 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 : 0.226 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 6 optimal weight: 9.9990 chunk 31 optimal weight: 0.0370 chunk 33 optimal weight: 7.9990 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.101006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.083681 restraints weight = 10061.500| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.31 r_work: 0.3107 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4999 Z= 0.094 Angle : 0.476 6.319 6794 Z= 0.237 Chirality : 0.039 0.170 722 Planarity : 0.004 0.053 861 Dihedral : 3.290 15.723 646 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.00 % Allowed : 10.40 % Favored : 87.60 % 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: 1.16 (0.35), residues: 594 helix: 1.86 (0.28), residues: 367 sheet: -2.81 (0.98), residues: 12 loop : -0.96 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.030 0.001 TYR A 50 PHE 0.008 0.001 PHE A 523 TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.09 ( 4989) covalent geometry : angle 0.47316 / 0.24 ( 6773) SS BOND : bond 0.00263 / 0.13 ( 3) SS BOND : angle 0.44332 / 0.27 ( 6) hydrogen bonds : bond 0.03033 / 2.07 ( 258) hydrogen bonds : angle 3.61917 / 2.70 ( 753) metal coordination : bond 0.00047 / 0.02 ( 2) link_BETA1-4 : bond 0.00300 / 0.16 ( 1) link_BETA1-4 : angle 1.36615 / 0.70 ( 3) link_NAG-ASN : bond 0.00125 / 0.06 ( 4) link_NAG-ASN : angle 1.11496 / 0.60 ( 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 63 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 GLN cc_start: 0.7701 (pm20) cc_final: 0.7318 (pp30) outliers start: 10 outliers final: 5 residues processed: 61 average time/residue: 0.0443 time to fit residues: 4.1002 Evaluate side-chains 51 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 509 ASP 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: 0.9980 chunk 41 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.099898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.082147 restraints weight = 10247.500| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.41 r_work: 0.3081 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4999 Z= 0.111 Angle : 0.507 6.332 6794 Z= 0.251 Chirality : 0.040 0.174 722 Planarity : 0.004 0.053 861 Dihedral : 3.381 15.760 646 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.20 % Allowed : 12.00 % 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: 1.25 (0.35), residues: 594 helix: 1.90 (0.28), residues: 368 sheet: -2.70 (1.03), residues: 12 loop : -0.86 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.024 0.001 TYR A 50 PHE 0.009 0.001 PHE A 400 TRP 0.010 0.001 TRP A 478 HIS 0.003 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 4989) covalent geometry : angle 0.50463 / 0.25 ( 6773) SS BOND : bond 0.00304 / 0.15 ( 3) SS BOND : angle 0.44771 / 0.27 ( 6) hydrogen bonds : bond 0.03123 / 2.13 ( 258) hydrogen bonds : angle 3.70553 / 2.77 ( 753) metal coordination : bond 0.00101 / 0.05 ( 2) link_BETA1-4 : bond 0.00298 / 0.16 ( 1) link_BETA1-4 : angle 1.39846 / 0.72 ( 3) link_NAG-ASN : bond 0.00088 / 0.04 ( 4) link_NAG-ASN : angle 1.17480 / 0.64 ( 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 53 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.0463 time to fit residues: 3.4598 Evaluate side-chains 49 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 194 TYR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 539 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 50 optimal weight: 0.0970 chunk 48 optimal weight: 0.0570 chunk 56 optimal weight: 0.0470 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.102479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.085251 restraints weight = 10015.056| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.31 r_work: 0.3142 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2771 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= 0.091 Angle : 0.495 7.239 6794 Z= 0.242 Chirality : 0.039 0.164 722 Planarity : 0.003 0.051 861 Dihedral : 3.261 15.355 646 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.00 % Allowed : 11.40 % Favored : 87.60 % 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: 1.35 (0.35), residues: 594 helix: 2.00 (0.28), residues: 367 sheet: -2.68 (1.03), residues: 12 loop : -0.85 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 514 TYR 0.024 0.001 TYR A 50 PHE 0.009 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/Z covalent geometry : bond 0.00198 / 0.09 ( 4989) covalent geometry : angle 0.49292 / 0.24 ( 6773) SS BOND : bond 0.00223 / 0.11 ( 3) SS BOND : angle 0.43642 / 0.27 ( 6) hydrogen bonds : bond 0.02905 / 1.98 ( 258) hydrogen bonds : angle 3.63005 / 2.72 ( 753) metal coordination : bond 0.00062 / 0.03 ( 2) link_BETA1-4 : bond 0.00327 / 0.17 ( 1) link_BETA1-4 : angle 1.08590 / 0.56 ( 3) link_NAG-ASN : bond 0.00217 / 0.11 ( 4) link_NAG-ASN : angle 1.07961 / 0.59 ( 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 54 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 GLN cc_start: 0.7817 (pm20) cc_final: 0.7359 (pp30) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 0.0437 time to fit residues: 3.5257 Evaluate side-chains 50 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 28 optimal weight: 0.9990 chunk 49 optimal weight: 0.0270 chunk 41 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.101452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.084097 restraints weight = 10097.752| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.37 r_work: 0.3113 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2827 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= 0.100 Angle : 0.497 6.998 6794 Z= 0.244 Chirality : 0.039 0.178 722 Planarity : 0.003 0.051 861 Dihedral : 3.257 16.403 646 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.00 % Allowed : 11.80 % 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: 1.47 (0.35), residues: 594 helix: 2.05 (0.28), residues: 367 sheet: -2.75 (1.15), residues: 10 loop : -0.73 (0.41), residues: 217 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 0.009 0.001 PHE A 315 TRP 0.009 0.001 TRP A 478 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 4989) covalent geometry : angle 0.49431 / 0.24 ( 6773) SS BOND : bond 0.00271 / 0.14 ( 3) SS BOND : angle 0.47288 / 0.29 ( 6) hydrogen bonds : bond 0.03018 / 2.06 ( 258) hydrogen bonds : angle 3.66565 / 2.74 ( 753) metal coordination : bond 0.00063 / 0.03 ( 2) link_BETA1-4 : bond 0.00150 / 0.08 ( 1) link_BETA1-4 : angle 1.29657 / 0.67 ( 3) link_NAG-ASN : bond 0.00097 / 0.05 ( 4) link_NAG-ASN : angle 1.17858 / 0.64 ( 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 54 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.0473 time to fit residues: 3.8343 Evaluate side-chains 50 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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: 0.0020 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.096514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.078828 restraints weight = 10106.873| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.35 r_work: 0.3015 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4999 Z= 0.195 Angle : 0.578 7.082 6794 Z= 0.292 Chirality : 0.043 0.168 722 Planarity : 0.004 0.054 861 Dihedral : 3.715 19.858 646 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.60 % Allowed : 12.00 % 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: 1.19 (0.35), residues: 594 helix: 1.79 (0.28), residues: 369 sheet: -2.39 (1.24), residues: 10 loop : -0.81 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 518 TYR 0.022 0.002 TYR A 50 PHE 0.017 0.002 PHE A 400 TRP 0.009 0.002 TRP A 168 HIS 0.008 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 ( 4989) covalent geometry : angle 0.57357 / 0.29 ( 6773) SS BOND : bond 0.00501 / 0.25 ( 3) SS BOND : angle 0.60852 / 0.37 ( 6) hydrogen bonds : bond 0.03780 / 2.58 ( 258) hydrogen bonds : angle 3.96926 / 2.95 ( 753) metal coordination : bond 0.00270 / 0.14 ( 2) link_BETA1-4 : bond 0.00014 / 0.01 ( 1) link_BETA1-4 : angle 1.81156 / 0.93 ( 3) link_NAG-ASN : bond 0.00233 / 0.12 ( 4) link_NAG-ASN : angle 1.52146 / 0.84 ( 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 46 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LEU cc_start: 0.8930 (tp) cc_final: 0.8719 (tp) outliers start: 3 outliers final: 3 residues processed: 45 average time/residue: 0.0505 time to fit residues: 3.4517 Evaluate side-chains 46 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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: 0.7980 chunk 12 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.098574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.081286 restraints weight = 10023.291| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.28 r_work: 0.3063 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4999 Z= 0.116 Angle : 0.530 7.316 6794 Z= 0.264 Chirality : 0.040 0.162 722 Planarity : 0.004 0.053 861 Dihedral : 3.530 17.901 646 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: 1.31 (0.35), residues: 594 helix: 1.88 (0.28), residues: 368 sheet: -2.45 (1.25), residues: 10 loop : -0.72 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 514 TYR 0.022 0.001 TYR A 50 PHE 0.010 0.001 PHE A 400 TRP 0.008 0.001 TRP A 168 HIS 0.003 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 4989) covalent geometry : angle 0.52677 / 0.26 ( 6773) SS BOND : bond 0.00349 / 0.17 ( 3) SS BOND : angle 0.53314 / 0.33 ( 6) hydrogen bonds : bond 0.03348 / 2.29 ( 258) hydrogen bonds : angle 3.83732 / 2.85 ( 753) metal coordination : bond 0.00052 / 0.03 ( 2) link_BETA1-4 : bond 0.00271 / 0.14 ( 1) link_BETA1-4 : angle 1.36989 / 0.71 ( 3) link_NAG-ASN : bond 0.00108 / 0.05 ( 4) link_NAG-ASN : angle 1.34303 / 0.75 ( 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 : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.0458 time to fit residues: 3.5184 Evaluate side-chains 50 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.098967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081615 restraints weight = 10035.751| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.32 r_work: 0.3070 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3186 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= 0.115 Angle : 0.526 7.335 6794 Z= 0.262 Chirality : 0.040 0.161 722 Planarity : 0.004 0.053 861 Dihedral : 3.468 17.940 646 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: 1.38 (0.35), residues: 594 helix: 1.92 (0.28), residues: 368 sheet: None (None), residues: 0 loop : -0.78 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 393 TYR 0.021 0.001 TYR A 50 PHE 0.010 0.001 PHE A 315 TRP 0.008 0.001 TRP A 168 HIS 0.003 0.001 HIS A 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 4989) covalent geometry : angle 0.52241 / 0.26 ( 6773) SS BOND : bond 0.00329 / 0.16 ( 3) SS BOND : angle 0.50517 / 0.31 ( 6) hydrogen bonds : bond 0.03285 / 2.24 ( 258) hydrogen bonds : angle 3.81433 / 2.83 ( 753) metal coordination : bond 0.00084 / 0.04 ( 2) link_BETA1-4 : bond 0.00289 / 0.15 ( 1) link_BETA1-4 : angle 1.35010 / 0.70 ( 3) link_NAG-ASN : bond 0.00100 / 0.05 ( 4) link_NAG-ASN : angle 1.35257 / 0.75 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1259.74 seconds wall clock time: 22 minutes 14.97 seconds (1334.97 seconds total)