Starting phenix.real_space_refine on Sat May 10 06:49:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bd8_44446/05_2025/9bd8_44446.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bd8_44446/05_2025/9bd8_44446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bd8_44446/05_2025/9bd8_44446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bd8_44446/05_2025/9bd8_44446.map" model { file = "/net/cci-nas-00/data/ceres_data/9bd8_44446/05_2025/9bd8_44446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bd8_44446/05_2025/9bd8_44446.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3406 2.51 5 N 880 2.21 5 O 1063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5369 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3423 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 24, 'TRANS': 437} Chain breaks: 7 Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 164 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 1, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "B" Number of atoms: 1932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1932 Classifications: {'peptide': 264} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 1 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 106 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.83, per 1000 atoms: 0.71 Number of scatterers: 5369 At special positions: 0 Unit cell: (61.42, 94.62, 129.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1063 8.00 N 880 7.00 C 3406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 39 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 390 " 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 NAG-ASN " NAG A4601 " - " ASN A 185 " Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 708.9 milliseconds 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1360 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 9 sheets defined 14.2% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 118 through 129 removed outlier: 4.327A pdb=" N TYR A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 139 Processing helix chain 'A' and resid 150 through 165 Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.832A pdb=" N ASN A 274 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 321 through 330 removed outlier: 3.872A pdb=" N VAL A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 334 Processing helix chain 'A' and resid 343 through 357 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 375 through 384 removed outlier: 3.863A pdb=" N GLN A 380 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 393 removed outlier: 4.282A pdb=" N THR A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 58 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 51 through 58 current: chain 'A' and resid 72 through 83 removed outlier: 6.836A pdb=" N ALA A 73 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU A 101 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG A 75 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A 99 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN A 77 " --> pdb=" O CYS A 97 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS A 97 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 112 " --> pdb=" O TYR A 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 111 through 115 current: chain 'A' and resid 142 through 144 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 142 through 144 current: chain 'A' and resid 186 through 195 removed outlier: 5.912A pdb=" N SER A 187 " --> pdb=" O ASP A 208 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASP A 208 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 206 " --> pdb=" O HIS A 189 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLU A 202 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG A 195 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA A 200 " --> pdb=" O ARG A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 829 through 839 removed outlier: 4.938A pdb=" N ILE A 830 " --> pdb=" O ILE A 854 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 854 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN A 845 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU A 942 " --> pdb=" O ILE A 953 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 961 through 962 Processing sheet with id=AA4, first strand: chain 'B' and resid 401 through 405 removed outlier: 6.085A pdb=" N LYS B 411 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N SER B 421 " --> pdb=" O LYS B 411 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 440 through 443 Processing sheet with id=AA6, first strand: chain 'B' and resid 476 through 482 removed outlier: 3.942A pdb=" N GLY B 478 " --> pdb=" O THR B 491 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 491 " --> pdb=" O GLY B 478 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 518 through 524 removed outlier: 5.921A pdb=" N THR B 534 " --> pdb=" O ARG B 520 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE B 522 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR B 532 " --> pdb=" O ILE B 522 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 563 through 568 removed outlier: 6.591A pdb=" N VAL B 578 " --> pdb=" O ASN B 564 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE B 566 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR B 576 " --> pdb=" O ILE B 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 612 through 614 181 hydrogen bonds defined for protein. 474 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1760 1.34 - 1.46: 1227 1.46 - 1.58: 2460 1.58 - 1.70: 0 1.70 - 1.82: 28 Bond restraints: 5475 Sorted by residual: bond pdb=" CA SER B 648 " pdb=" C SER B 648 " ideal model delta sigma weight residual 1.531 1.523 0.008 7.40e-03 1.83e+04 1.30e+00 bond pdb=" CA SER B 648 " pdb=" CB SER B 648 " ideal model delta sigma weight residual 1.522 1.529 -0.007 7.00e-03 2.04e+04 1.01e+00 bond pdb=" N ALA B 437 " pdb=" CA ALA B 437 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 8.85e-01 bond pdb=" N ASN B 425 " pdb=" CA ASN B 425 " ideal model delta sigma weight residual 1.457 1.468 -0.010 1.29e-02 6.01e+03 6.35e-01 bond pdb=" CB PRO B 519 " pdb=" CG PRO B 519 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.88e-01 ... (remaining 5470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 7141 1.32 - 2.63: 282 2.63 - 3.95: 47 3.95 - 5.26: 10 5.26 - 6.58: 6 Bond angle restraints: 7486 Sorted by residual: angle pdb=" C ALA B 437 " pdb=" CA ALA B 437 " pdb=" CB ALA B 437 " ideal model delta sigma weight residual 110.42 115.72 -5.30 1.99e+00 2.53e-01 7.08e+00 angle pdb=" N LEU A 268 " pdb=" CA LEU A 268 " pdb=" C LEU A 268 " ideal model delta sigma weight residual 109.81 115.67 -5.86 2.21e+00 2.05e-01 7.02e+00 angle pdb=" C GLN B 561 " pdb=" N TRP B 562 " pdb=" CA TRP B 562 " ideal model delta sigma weight residual 121.80 126.80 -5.00 2.44e+00 1.68e-01 4.20e+00 angle pdb=" N ILE B 624 " pdb=" CA ILE B 624 " pdb=" C ILE B 624 " ideal model delta sigma weight residual 112.35 109.50 2.85 1.41e+00 5.03e-01 4.09e+00 angle pdb=" C ILE B 451 " pdb=" N CYS B 452 " pdb=" CA CYS B 452 " ideal model delta sigma weight residual 122.08 118.62 3.46 1.84e+00 2.95e-01 3.53e+00 ... (remaining 7481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 2943 17.13 - 34.27: 253 34.27 - 51.40: 44 51.40 - 68.53: 6 68.53 - 85.66: 3 Dihedral angle restraints: 3249 sinusoidal: 1151 harmonic: 2098 Sorted by residual: dihedral pdb=" CB CYS A 385 " pdb=" SG CYS A 385 " pdb=" SG CYS A 390 " pdb=" CB CYS A 390 " ideal model delta sinusoidal sigma weight residual 93.00 42.65 50.35 1 1.00e+01 1.00e-02 3.47e+01 dihedral pdb=" CB CYS A 245 " pdb=" SG CYS A 245 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual 93.00 47.91 45.09 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CA LEU A 288 " pdb=" C LEU A 288 " pdb=" N GLU A 289 " pdb=" CA GLU A 289 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 3246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 580 0.034 - 0.068: 204 0.068 - 0.102: 82 0.102 - 0.135: 33 0.135 - 0.169: 3 Chirality restraints: 902 Sorted by residual: chirality pdb=" CA ILE A 830 " pdb=" N ILE A 830 " pdb=" C ILE A 830 " pdb=" CB ILE A 830 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA ILE A 891 " pdb=" N ILE A 891 " pdb=" C ILE A 891 " pdb=" CB ILE A 891 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ILE A 91 " pdb=" N ILE A 91 " pdb=" C ILE A 91 " pdb=" CB ILE A 91 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 899 not shown) Planarity restraints: 965 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 562 " 0.017 2.00e-02 2.50e+03 1.32e-02 4.36e+00 pdb=" CG TRP B 562 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP B 562 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 562 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 562 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 562 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 562 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 562 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 562 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 562 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 855 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.16e+00 pdb=" N PRO A 856 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 856 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 856 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 619 " -0.011 2.00e-02 2.50e+03 8.73e-03 1.33e+00 pdb=" CG PHE B 619 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE B 619 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 619 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 619 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 619 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 619 " -0.001 2.00e-02 2.50e+03 ... (remaining 962 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 237 2.69 - 3.24: 6075 3.24 - 3.80: 9493 3.80 - 4.35: 11963 4.35 - 4.90: 18465 Nonbonded interactions: 46233 Sorted by model distance: nonbonded pdb=" OG SER A 937 " pdb=" O LEU A1001 " model vdw 2.141 3.040 nonbonded pdb=" O ALA A 163 " pdb=" OH TYR A 247 " model vdw 2.146 3.040 nonbonded pdb=" OG SER A 60 " pdb=" OG1 THR A 74 " model vdw 2.181 3.040 nonbonded pdb=" O SER B 470 " pdb=" NH1 ARG B 508 " model vdw 2.210 3.120 nonbonded pdb=" O LEU A 268 " pdb=" OG SER A 271 " model vdw 2.216 3.040 ... (remaining 46228 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.960 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.003 0.038 5481 Z= 0.130 Angle : 0.628 6.575 7499 Z= 0.328 Chirality : 0.044 0.169 902 Planarity : 0.003 0.037 964 Dihedral : 13.216 85.664 1874 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.32), residues: 706 helix: 1.25 (0.69), residues: 76 sheet: -1.26 (0.32), residues: 253 loop : -2.19 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 562 HIS 0.008 0.002 HIS A 265 PHE 0.020 0.002 PHE B 619 TYR 0.012 0.001 TYR B 442 ARG 0.002 0.000 ARG B 574 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 1) link_NAG-ASN : angle 1.82363 ( 3) hydrogen bonds : bond 0.17034 ( 181) hydrogen bonds : angle 8.48671 ( 474) SS BOND : bond 0.00150 ( 5) SS BOND : angle 1.34659 ( 10) covalent geometry : bond 0.00269 ( 5475) covalent geometry : angle 0.62578 ( 7486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1390 time to fit residues: 6.1465 Evaluate side-chains 25 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 0.0970 chunk 65 optimal weight: 5.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.033959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.026203 restraints weight = 67304.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.027063 restraints weight = 49724.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.027727 restraints weight = 39477.081| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5481 Z= 0.140 Angle : 0.602 6.243 7499 Z= 0.318 Chirality : 0.043 0.150 902 Planarity : 0.004 0.040 964 Dihedral : 5.245 18.556 775 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.31), residues: 706 helix: 1.25 (0.66), residues: 79 sheet: -1.39 (0.32), residues: 251 loop : -2.31 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 562 HIS 0.003 0.001 HIS B 607 PHE 0.013 0.002 PHE A 831 TYR 0.037 0.002 TYR B 442 ARG 0.004 0.001 ARG A 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 1) link_NAG-ASN : angle 1.66674 ( 3) hydrogen bonds : bond 0.03553 ( 181) hydrogen bonds : angle 7.34194 ( 474) SS BOND : bond 0.00261 ( 5) SS BOND : angle 1.36943 ( 10) covalent geometry : bond 0.00296 ( 5475) covalent geometry : angle 0.59994 ( 7486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1299 time to fit residues: 5.9105 Evaluate side-chains 24 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.031910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.024950 restraints weight = 72013.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.025764 restraints weight = 52817.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.026377 restraints weight = 41519.363| |-----------------------------------------------------------------------------| r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5481 Z= 0.262 Angle : 0.727 7.576 7499 Z= 0.384 Chirality : 0.046 0.169 902 Planarity : 0.004 0.045 964 Dihedral : 5.877 21.985 775 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 29.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.30), residues: 706 helix: 0.88 (0.64), residues: 79 sheet: -1.71 (0.31), residues: 239 loop : -2.56 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 562 HIS 0.004 0.001 HIS B 607 PHE 0.019 0.003 PHE A 270 TYR 0.031 0.002 TYR B 442 ARG 0.006 0.001 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.01491 ( 1) link_NAG-ASN : angle 4.54543 ( 3) hydrogen bonds : bond 0.04301 ( 181) hydrogen bonds : angle 7.57982 ( 474) SS BOND : bond 0.00428 ( 5) SS BOND : angle 1.71812 ( 10) covalent geometry : bond 0.00519 ( 5475) covalent geometry : angle 0.71909 ( 7486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9472 (mp) cc_final: 0.9011 (tp) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1103 time to fit residues: 4.7712 Evaluate side-chains 22 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 11 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 70 optimal weight: 0.0370 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 0.0070 chunk 64 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN A 349 ASN A 902 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.034142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.026355 restraints weight = 68874.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.027239 restraints weight = 50951.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.027896 restraints weight = 40439.099| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5481 Z= 0.122 Angle : 0.634 6.607 7499 Z= 0.327 Chirality : 0.045 0.153 902 Planarity : 0.004 0.046 964 Dihedral : 5.407 18.773 775 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.31), residues: 706 helix: 1.20 (0.66), residues: 75 sheet: -1.63 (0.31), residues: 260 loop : -2.40 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 562 HIS 0.004 0.001 HIS A 828 PHE 0.014 0.002 PHE A 267 TYR 0.025 0.002 TYR B 442 ARG 0.004 0.000 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 1) link_NAG-ASN : angle 1.88447 ( 3) hydrogen bonds : bond 0.03098 ( 181) hydrogen bonds : angle 7.06269 ( 474) SS BOND : bond 0.00209 ( 5) SS BOND : angle 1.53373 ( 10) covalent geometry : bond 0.00266 ( 5475) covalent geometry : angle 0.63135 ( 7486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9487 (mp) cc_final: 0.9038 (tp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1401 time to fit residues: 6.5651 Evaluate side-chains 24 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 0.0970 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.032480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.025177 restraints weight = 69922.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.025983 restraints weight = 51917.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.026593 restraints weight = 41339.023| |-----------------------------------------------------------------------------| r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5481 Z= 0.236 Angle : 0.682 6.970 7499 Z= 0.361 Chirality : 0.044 0.189 902 Planarity : 0.004 0.047 964 Dihedral : 5.715 20.922 775 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 26.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.30), residues: 706 helix: 0.81 (0.61), residues: 85 sheet: -1.71 (0.31), residues: 249 loop : -2.69 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 562 HIS 0.003 0.001 HIS A 907 PHE 0.022 0.003 PHE A 831 TYR 0.028 0.002 TYR B 442 ARG 0.004 0.001 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 1) link_NAG-ASN : angle 2.26580 ( 3) hydrogen bonds : bond 0.03776 ( 181) hydrogen bonds : angle 7.38397 ( 474) SS BOND : bond 0.00413 ( 5) SS BOND : angle 1.68760 ( 10) covalent geometry : bond 0.00473 ( 5475) covalent geometry : angle 0.67824 ( 7486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 652 MET cc_start: 0.8974 (mmm) cc_final: 0.8186 (tpp) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1480 time to fit residues: 5.9954 Evaluate side-chains 21 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN B 548 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.032606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.025190 restraints weight = 69785.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.026030 restraints weight = 51248.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.026656 restraints weight = 40516.849| |-----------------------------------------------------------------------------| r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5481 Z= 0.205 Angle : 0.676 7.367 7499 Z= 0.354 Chirality : 0.045 0.169 902 Planarity : 0.004 0.047 964 Dihedral : 5.750 21.224 775 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 25.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.31), residues: 706 helix: 0.82 (0.62), residues: 85 sheet: -1.70 (0.32), residues: 247 loop : -2.72 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 562 HIS 0.003 0.001 HIS A 189 PHE 0.017 0.002 PHE A 831 TYR 0.027 0.002 TYR B 442 ARG 0.003 0.001 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 1) link_NAG-ASN : angle 1.88541 ( 3) hydrogen bonds : bond 0.03523 ( 181) hydrogen bonds : angle 7.41998 ( 474) SS BOND : bond 0.00374 ( 5) SS BOND : angle 1.70433 ( 10) covalent geometry : bond 0.00417 ( 5475) covalent geometry : angle 0.67267 ( 7486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 442 TYR cc_start: 0.8131 (m-80) cc_final: 0.7762 (m-80) REVERT: B 652 MET cc_start: 0.9004 (mmm) cc_final: 0.8519 (tpp) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1455 time to fit residues: 5.8196 Evaluate side-chains 20 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 0.0370 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.033754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.026119 restraints weight = 67610.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.026978 restraints weight = 49921.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.027628 restraints weight = 39543.281| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5481 Z= 0.123 Angle : 0.633 8.490 7499 Z= 0.322 Chirality : 0.044 0.231 902 Planarity : 0.004 0.042 964 Dihedral : 5.430 18.235 775 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.31), residues: 706 helix: 1.00 (0.65), residues: 75 sheet: -1.57 (0.32), residues: 245 loop : -2.53 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 562 HIS 0.007 0.001 HIS A 265 PHE 0.016 0.002 PHE A 831 TYR 0.016 0.002 TYR B 442 ARG 0.003 0.000 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 1) link_NAG-ASN : angle 5.25077 ( 3) hydrogen bonds : bond 0.02934 ( 181) hydrogen bonds : angle 7.05292 ( 474) SS BOND : bond 0.00285 ( 5) SS BOND : angle 1.60100 ( 10) covalent geometry : bond 0.00270 ( 5475) covalent geometry : angle 0.62230 ( 7486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 442 TYR cc_start: 0.7982 (m-80) cc_final: 0.7662 (m-80) REVERT: B 525 ASP cc_start: 0.9088 (m-30) cc_final: 0.8868 (t70) REVERT: B 585 ILE cc_start: 0.9465 (mp) cc_final: 0.8999 (tp) REVERT: B 652 MET cc_start: 0.8711 (mmm) cc_final: 0.8109 (tpp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1407 time to fit residues: 6.3249 Evaluate side-chains 24 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 0.0570 chunk 71 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN B 665 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.032807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.025318 restraints weight = 69067.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.026168 restraints weight = 50524.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.026812 restraints weight = 39732.450| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5481 Z= 0.189 Angle : 0.654 6.634 7499 Z= 0.342 Chirality : 0.044 0.206 902 Planarity : 0.004 0.043 964 Dihedral : 5.564 20.392 775 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.31), residues: 706 helix: 0.95 (0.61), residues: 79 sheet: -1.72 (0.32), residues: 245 loop : -2.51 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 562 HIS 0.008 0.001 HIS A 265 PHE 0.017 0.002 PHE A 831 TYR 0.025 0.002 TYR B 442 ARG 0.003 0.001 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 1) link_NAG-ASN : angle 3.75151 ( 3) hydrogen bonds : bond 0.03340 ( 181) hydrogen bonds : angle 7.13417 ( 474) SS BOND : bond 0.00369 ( 5) SS BOND : angle 1.65182 ( 10) covalent geometry : bond 0.00386 ( 5475) covalent geometry : angle 0.64763 ( 7486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 442 TYR cc_start: 0.8128 (m-80) cc_final: 0.7863 (m-80) REVERT: B 525 ASP cc_start: 0.9139 (m-30) cc_final: 0.8913 (t70) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1501 time to fit residues: 5.7637 Evaluate side-chains 21 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.033398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.025692 restraints weight = 68123.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.026541 restraints weight = 50521.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.027189 restraints weight = 40151.606| |-----------------------------------------------------------------------------| r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5481 Z= 0.146 Angle : 0.631 6.488 7499 Z= 0.325 Chirality : 0.044 0.192 902 Planarity : 0.004 0.040 964 Dihedral : 5.449 18.957 775 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.31), residues: 706 helix: 0.70 (0.60), residues: 85 sheet: -1.67 (0.32), residues: 256 loop : -2.49 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 562 HIS 0.008 0.001 HIS A 265 PHE 0.016 0.002 PHE A 831 TYR 0.020 0.002 TYR B 442 ARG 0.002 0.000 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 1) link_NAG-ASN : angle 3.12533 ( 3) hydrogen bonds : bond 0.03002 ( 181) hydrogen bonds : angle 7.01772 ( 474) SS BOND : bond 0.00328 ( 5) SS BOND : angle 1.64748 ( 10) covalent geometry : bond 0.00315 ( 5475) covalent geometry : angle 0.62598 ( 7486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 442 TYR cc_start: 0.8032 (m-80) cc_final: 0.7748 (m-80) REVERT: B 525 ASP cc_start: 0.9157 (m-30) cc_final: 0.8909 (t70) REVERT: B 585 ILE cc_start: 0.9448 (mp) cc_final: 0.9002 (tp) REVERT: B 652 MET cc_start: 0.8828 (mmm) cc_final: 0.8283 (tpp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1344 time to fit residues: 6.0193 Evaluate side-chains 23 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.0370 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 41 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.033672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.026072 restraints weight = 68095.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.026916 restraints weight = 50640.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.027548 restraints weight = 40349.455| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5481 Z= 0.136 Angle : 0.618 6.570 7499 Z= 0.317 Chirality : 0.044 0.188 902 Planarity : 0.004 0.041 964 Dihedral : 5.322 18.512 775 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.31), residues: 706 helix: 0.51 (0.59), residues: 85 sheet: -1.63 (0.32), residues: 256 loop : -2.43 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 562 HIS 0.007 0.001 HIS A 265 PHE 0.015 0.002 PHE A 831 TYR 0.019 0.002 TYR B 442 ARG 0.004 0.000 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 1) link_NAG-ASN : angle 2.70890 ( 3) hydrogen bonds : bond 0.02927 ( 181) hydrogen bonds : angle 6.87555 ( 474) SS BOND : bond 0.00311 ( 5) SS BOND : angle 1.64411 ( 10) covalent geometry : bond 0.00296 ( 5475) covalent geometry : angle 0.61344 ( 7486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 442 TYR cc_start: 0.8008 (m-80) cc_final: 0.7718 (m-80) REVERT: B 525 ASP cc_start: 0.9177 (m-30) cc_final: 0.8912 (t70) REVERT: B 652 MET cc_start: 0.8833 (mmm) cc_final: 0.8132 (tpp) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1470 time to fit residues: 5.8699 Evaluate side-chains 21 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 12 optimal weight: 0.0060 chunk 11 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN B 632 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.033648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.025945 restraints weight = 68702.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.026785 restraints weight = 51107.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.027437 restraints weight = 40699.163| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5481 Z= 0.139 Angle : 0.626 7.599 7499 Z= 0.318 Chirality : 0.044 0.182 902 Planarity : 0.004 0.041 964 Dihedral : 5.258 18.742 775 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.31), residues: 706 helix: 0.85 (0.61), residues: 81 sheet: -1.78 (0.31), residues: 261 loop : -2.29 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 562 HIS 0.006 0.001 HIS A 265 PHE 0.016 0.002 PHE A 831 TYR 0.020 0.002 TYR B 442 ARG 0.002 0.000 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 1) link_NAG-ASN : angle 2.52983 ( 3) hydrogen bonds : bond 0.02906 ( 181) hydrogen bonds : angle 6.87383 ( 474) SS BOND : bond 0.00308 ( 5) SS BOND : angle 1.60609 ( 10) covalent geometry : bond 0.00298 ( 5475) covalent geometry : angle 0.62127 ( 7486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1868.59 seconds wall clock time: 33 minutes 37.98 seconds (2017.98 seconds total)