Starting phenix.real_space_refine on Sun Apr 27 10:43:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bd8_44446/04_2025/9bd8_44446.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bd8_44446/04_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_44446/04_2025/9bd8_44446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bd8_44446/04_2025/9bd8_44446.map" model { file = "/net/cci-nas-00/data/ceres_data/9bd8_44446/04_2025/9bd8_44446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bd8_44446/04_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-5669/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: 4.11, per 1000 atoms: 0.77 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: 1.43 Conformation dependent library (CDL) restraints added in 707.1 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: 0.72 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: 2.07 Time building geometry restraints manager: 1.69 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: 1.620 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.570 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.600 ------------------------------------------------------------------------------- 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 : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1552 time to fit residues: 6.9355 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 : 0.643 ------------------------------------------------------------------------------- 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 = 67305.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.027063 restraints weight = 49720.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.027730 restraints weight = 39480.109| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 0.029 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 1.66675 ( 3) hydrogen bonds : bond 0.03553 ( 181) hydrogen bonds : angle 7.34199 ( 474) SS BOND : bond 0.00261 ( 5) SS BOND : angle 1.36948 ( 10) covalent geometry : bond 0.00296 ( 5475) covalent geometry : angle 0.59995 ( 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 : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1412 time to fit residues: 6.4552 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 : 0.627 ------------------------------------------------------------------------------- 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: 0.3980 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: 0.9980 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 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 = 0.2851 r_free = 0.2851 target = 0.032171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.025322 restraints weight = 71755.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.026121 restraints weight = 52859.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.026728 restraints weight = 41779.590| |-----------------------------------------------------------------------------| r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5481 Z= 0.246 Angle : 0.698 8.466 7499 Z= 0.369 Chirality : 0.045 0.147 902 Planarity : 0.004 0.044 964 Dihedral : 5.716 21.383 775 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 28.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % 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: -2.68 (0.30), residues: 706 helix: 0.97 (0.65), residues: 79 sheet: -1.65 (0.32), residues: 238 loop : -2.52 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 562 HIS 0.003 0.001 HIS B 607 PHE 0.016 0.003 PHE B 402 TYR 0.027 0.002 TYR B 442 ARG 0.007 0.001 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00849 ( 1) link_NAG-ASN : angle 5.01770 ( 3) hydrogen bonds : bond 0.04110 ( 181) hydrogen bonds : angle 7.49455 ( 474) SS BOND : bond 0.00390 ( 5) SS BOND : angle 1.62661 ( 10) covalent geometry : bond 0.00491 ( 5475) covalent geometry : angle 0.68914 ( 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 27 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.588 Fit side-chains REVERT: B 585 ILE cc_start: 0.9465 (mp) cc_final: 0.9002 (tp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.1048 time to fit residues: 4.8737 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 : 0.588 ------------------------------------------------------------------------------- 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: 0.9990 chunk 37 optimal weight: 4.9990 chunk 70 optimal weight: 0.0670 chunk 23 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.3318 ------------------------------------------------------------------------------- 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 = 0.2924 r_free = 0.2924 target = 0.034244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.026485 restraints weight = 68848.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.027369 restraints weight = 50398.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.028051 restraints weight = 39685.551| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1459 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= 0.119 Angle : 0.629 6.717 7499 Z= 0.323 Chirality : 0.044 0.154 902 Planarity : 0.004 0.047 964 Dihedral : 5.339 18.371 775 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 18.26 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: -2.51 (0.31), residues: 706 helix: 1.27 (0.67), residues: 75 sheet: -1.55 (0.31), residues: 258 loop : -2.42 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 562 HIS 0.004 0.001 HIS B 607 PHE 0.016 0.002 PHE A 894 TYR 0.020 0.002 TYR B 442 ARG 0.006 0.001 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 1) link_NAG-ASN : angle 2.19670 ( 3) hydrogen bonds : bond 0.03073 ( 181) hydrogen bonds : angle 7.01702 ( 474) SS BOND : bond 0.00245 ( 5) SS BOND : angle 1.57258 ( 10) covalent geometry : bond 0.00258 ( 5475) covalent geometry : angle 0.62528 ( 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 : 0.669 Fit side-chains revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9423 (mp) cc_final: 0.9001 (tp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1499 time to fit residues: 6.7477 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 : 0.580 ------------------------------------------------------------------------------- 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: 0.0000 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.033193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.025668 restraints weight = 67943.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.026527 restraints weight = 49809.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.027185 restraints weight = 39084.260| |-----------------------------------------------------------------------------| r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5481 Z= 0.174 Angle : 0.626 6.759 7499 Z= 0.328 Chirality : 0.044 0.201 902 Planarity : 0.004 0.044 964 Dihedral : 5.386 19.431 775 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % 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: -2.57 (0.31), residues: 706 helix: 1.03 (0.65), residues: 79 sheet: -1.50 (0.31), residues: 258 loop : -2.53 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 562 HIS 0.002 0.001 HIS A 828 PHE 0.020 0.002 PHE A 831 TYR 0.011 0.002 TYR B 442 ARG 0.005 0.001 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 1) link_NAG-ASN : angle 2.05783 ( 3) hydrogen bonds : bond 0.03291 ( 181) hydrogen bonds : angle 7.11448 ( 474) SS BOND : bond 0.00329 ( 5) SS BOND : angle 1.66308 ( 10) covalent geometry : bond 0.00358 ( 5475) covalent geometry : angle 0.62254 ( 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 28 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9435 (mp) cc_final: 0.8974 (tp) REVERT: B 652 MET cc_start: 0.8947 (mmm) cc_final: 0.7849 (tpp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1442 time to fit residues: 6.2978 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 : 0.606 ------------------------------------------------------------------------------- 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: 0.9990 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.033378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.025779 restraints weight = 68421.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.026650 restraints weight = 50016.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.027309 restraints weight = 39313.209| |-----------------------------------------------------------------------------| r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1721 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= 0.167 Angle : 0.634 7.433 7499 Z= 0.327 Chirality : 0.044 0.169 902 Planarity : 0.004 0.043 964 Dihedral : 5.398 20.062 775 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % 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: -2.58 (0.31), residues: 706 helix: 1.07 (0.63), residues: 81 sheet: -1.54 (0.31), residues: 258 loop : -2.53 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 562 HIS 0.002 0.001 HIS A 828 PHE 0.017 0.002 PHE A 831 TYR 0.015 0.002 TYR B 442 ARG 0.003 0.000 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 1) link_NAG-ASN : angle 1.82607 ( 3) hydrogen bonds : bond 0.03193 ( 181) hydrogen bonds : angle 7.10926 ( 474) SS BOND : bond 0.00318 ( 5) SS BOND : angle 1.66098 ( 10) covalent geometry : bond 0.00347 ( 5475) covalent geometry : angle 0.63025 ( 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 29 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9439 (mp) cc_final: 0.8965 (tp) REVERT: B 652 MET cc_start: 0.8948 (mmm) cc_final: 0.8323 (tpp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1404 time to fit residues: 6.3117 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 : 0.642 ------------------------------------------------------------------------------- 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: 0.0570 chunk 60 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 0.0870 chunk 38 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 52 optimal weight: 0.0470 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- 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 A 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.034282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.026437 restraints weight = 66644.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.027327 restraints weight = 48868.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.028008 restraints weight = 38624.696| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5481 Z= 0.111 Angle : 0.622 8.235 7499 Z= 0.314 Chirality : 0.045 0.257 902 Planarity : 0.003 0.041 964 Dihedral : 5.129 17.649 775 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.18 % Allowed : 2.86 % Favored : 96.96 % 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: -2.51 (0.31), residues: 706 helix: 0.93 (0.63), residues: 81 sheet: -1.42 (0.32), residues: 248 loop : -2.49 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 562 HIS 0.003 0.001 HIS A 828 PHE 0.016 0.002 PHE A 831 TYR 0.011 0.001 TYR B 442 ARG 0.002 0.000 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 1) link_NAG-ASN : angle 5.43885 ( 3) hydrogen bonds : bond 0.02778 ( 181) hydrogen bonds : angle 6.80022 ( 474) SS BOND : bond 0.00260 ( 5) SS BOND : angle 1.58048 ( 10) covalent geometry : bond 0.00245 ( 5475) covalent geometry : angle 0.61071 ( 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: 1 poor density : 28 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9467 (mp) cc_final: 0.9014 (tp) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.1397 time to fit residues: 6.2773 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 : 0.617 ------------------------------------------------------------------------------- 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: 0.4980 chunk 43 optimal weight: 2.9990 chunk 71 optimal weight: 0.0070 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 0.1980 chunk 47 optimal weight: 4.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- 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 211 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 = 0.2882 r_free = 0.2882 target = 0.033214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.025595 restraints weight = 68676.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.026448 restraints weight = 50568.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.027081 restraints weight = 40061.122| |-----------------------------------------------------------------------------| r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1903 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= 0.180 Angle : 0.637 6.595 7499 Z= 0.332 Chirality : 0.044 0.202 902 Planarity : 0.004 0.040 964 Dihedral : 5.319 19.519 775 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: -2.59 (0.31), residues: 706 helix: 0.81 (0.61), residues: 81 sheet: -1.54 (0.31), residues: 259 loop : -2.48 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 562 HIS 0.002 0.001 HIS A 907 PHE 0.017 0.002 PHE A 831 TYR 0.020 0.002 TYR B 442 ARG 0.003 0.000 ARG B 574 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 1) link_NAG-ASN : angle 3.61354 ( 3) hydrogen bonds : bond 0.03189 ( 181) hydrogen bonds : angle 6.96247 ( 474) SS BOND : bond 0.00385 ( 5) SS BOND : angle 1.78163 ( 10) covalent geometry : bond 0.00369 ( 5475) covalent geometry : angle 0.62963 ( 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 29 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9452 (mp) cc_final: 0.8986 (tp) REVERT: B 652 MET cc_start: 0.8869 (mmm) cc_final: 0.7740 (tpp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1359 time to fit residues: 6.0823 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 : 0.585 ------------------------------------------------------------------------------- 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: 1.9990 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.2896 r_free = 0.2896 target = 0.033475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.025745 restraints weight = 67517.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.026593 restraints weight = 49977.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.027236 restraints weight = 39589.479| |-----------------------------------------------------------------------------| r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5481 Z= 0.156 Angle : 0.626 6.499 7499 Z= 0.323 Chirality : 0.044 0.196 902 Planarity : 0.004 0.042 964 Dihedral : 5.334 19.616 775 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: -2.57 (0.31), residues: 706 helix: 0.91 (0.62), residues: 81 sheet: -1.58 (0.32), residues: 258 loop : -2.44 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 562 HIS 0.008 0.001 HIS A 265 PHE 0.016 0.002 PHE A 831 TYR 0.018 0.002 TYR B 442 ARG 0.002 0.000 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 1) link_NAG-ASN : angle 2.99907 ( 3) hydrogen bonds : bond 0.02983 ( 181) hydrogen bonds : angle 6.95979 ( 474) SS BOND : bond 0.00353 ( 5) SS BOND : angle 1.67431 ( 10) covalent geometry : bond 0.00328 ( 5475) covalent geometry : angle 0.62113 ( 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 28 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 585 ILE cc_start: 0.9460 (mp) cc_final: 0.9000 (tp) REVERT: B 652 MET cc_start: 0.8925 (mmm) cc_final: 0.7857 (tpp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1484 time to fit residues: 6.5276 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 : 0.655 ------------------------------------------------------------------------------- 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: 0.6980 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 0.0060 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 211 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 = 0.2906 r_free = 0.2906 target = 0.033714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.025874 restraints weight = 66721.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.026743 restraints weight = 49340.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.027396 restraints weight = 39017.360| |-----------------------------------------------------------------------------| r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1992 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= 0.140 Angle : 0.628 6.441 7499 Z= 0.321 Chirality : 0.044 0.195 902 Planarity : 0.004 0.041 964 Dihedral : 5.293 19.001 775 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -2.51 (0.31), residues: 706 helix: 0.95 (0.62), residues: 81 sheet: -1.62 (0.31), residues: 265 loop : -2.33 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 562 HIS 0.009 0.001 HIS A 265 PHE 0.015 0.002 PHE A 831 TYR 0.017 0.002 TYR B 442 ARG 0.002 0.000 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 1) link_NAG-ASN : angle 2.63233 ( 3) hydrogen bonds : bond 0.02870 ( 181) hydrogen bonds : angle 6.88808 ( 474) SS BOND : bond 0.00336 ( 5) SS BOND : angle 1.67073 ( 10) covalent geometry : bond 0.00297 ( 5475) covalent geometry : angle 0.62354 ( 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 28 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 525 ASP cc_start: 0.9134 (m-30) cc_final: 0.8899 (t70) REVERT: B 585 ILE cc_start: 0.9458 (mp) cc_final: 0.9008 (tp) REVERT: B 652 MET cc_start: 0.8855 (mmm) cc_final: 0.7817 (tpp) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1447 time to fit residues: 6.3135 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 : 0.676 ------------------------------------------------------------------------------- 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: 0.0030 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.0040 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 overall best weight: 0.4402 ------------------------------------------------------------------------------- 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 211 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 = 0.2927 r_free = 0.2927 target = 0.034321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.026405 restraints weight = 67055.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.027336 restraints weight = 48474.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.028047 restraints weight = 37699.988| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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 0.030 5481 Z= 0.116 Angle : 0.612 6.293 7499 Z= 0.310 Chirality : 0.044 0.196 902 Planarity : 0.003 0.040 964 Dihedral : 5.126 17.664 775 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -2.49 (0.31), residues: 706 helix: 0.79 (0.62), residues: 81 sheet: -1.70 (0.31), residues: 272 loop : -2.18 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 562 HIS 0.008 0.001 HIS A 265 PHE 0.015 0.001 PHE A 831 TYR 0.013 0.001 TYR B 442 ARG 0.002 0.000 ARG A 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 1) link_NAG-ASN : angle 2.33209 ( 3) hydrogen bonds : bond 0.02686 ( 181) hydrogen bonds : angle 6.70973 ( 474) SS BOND : bond 0.00294 ( 5) SS BOND : angle 1.62726 ( 10) covalent geometry : bond 0.00255 ( 5475) covalent geometry : angle 0.60738 ( 7486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2010.89 seconds wall clock time: 35 minutes 37.49 seconds (2137.49 seconds total)