Starting phenix.real_space_refine on Thu Jul 24 19:51:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vrh_21368/07_2025/6vrh_21368.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vrh_21368/07_2025/6vrh_21368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vrh_21368/07_2025/6vrh_21368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vrh_21368/07_2025/6vrh_21368.map" model { file = "/net/cci-nas-00/data/ceres_data/6vrh_21368/07_2025/6vrh_21368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vrh_21368/07_2025/6vrh_21368.cif" } resolution = 3.3 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= -0.001 sd= 0.946 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 92 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 C 4045 2.51 5 N 958 2.21 5 O 1103 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6142 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4311 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 517} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "B" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 924 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 88 Unusual residues: {' CL': 1, '8PR': 1, 'LMT': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.80, per 1000 atoms: 0.78 Number of scatterers: 6142 At special positions: 0 Unit cell: (96.552, 103.032, 81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 F 1 9.00 O 1103 8.00 N 958 7.00 C 4045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " 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 A 701 " - " ASN A 208 " " NAG A 704 " - " ASN A 217 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 870.3 milliseconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 57.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.752A pdb=" N PHE A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 89 " --> pdb=" O LYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 113 through 116 removed outlier: 3.525A pdb=" N ALA A 116 " --> pdb=" O GLY A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 128 through 144 removed outlier: 3.858A pdb=" N LEU A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.639A pdb=" N ARG A 152 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 159 through 190 removed outlier: 4.250A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE A 179 " --> pdb=" O TYR A 175 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.653A pdb=" N THR A 198 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 199 " --> pdb=" O PRO A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 199' Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 238 through 242 removed outlier: 3.701A pdb=" N ARG A 241 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 271 removed outlier: 3.591A pdb=" N ALA A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 removed outlier: 4.155A pdb=" N LYS A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.698A pdb=" N ILE A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 removed outlier: 4.354A pdb=" N GLY A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 removed outlier: 3.546A pdb=" N LEU A 321 " --> pdb=" O GLN A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 322 through 338 removed outlier: 4.248A pdb=" N TRP A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 350 removed outlier: 3.565A pdb=" N TYR A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 390 removed outlier: 3.688A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 removed outlier: 3.631A pdb=" N VAL A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'A' and resid 419 through 454 removed outlier: 3.694A pdb=" N PHE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 478 removed outlier: 3.657A pdb=" N VAL A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 481 No H-bonds generated for 'chain 'A' and resid 479 through 481' Processing helix chain 'A' and resid 484 through 496 removed outlier: 3.758A pdb=" N VAL A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 514 Processing helix chain 'A' and resid 517 through 530 Processing helix chain 'A' and resid 534 through 543 Processing helix chain 'A' and resid 543 through 559 removed outlier: 3.777A pdb=" N SER A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 587 removed outlier: 4.045A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 removed outlier: 3.546A pdb=" N TYR A 592 " --> pdb=" O CYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 612 removed outlier: 3.740A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.931A pdb=" N TYR B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.877A pdb=" N LYS B 84 " --> pdb=" O GLN B 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 26 removed outlier: 6.553A pdb=" N THR C 89 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 11.180A pdb=" N GLN C 47 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N SER C 87 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 12.093A pdb=" N VAL C 49 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 11.818A pdb=" N SER C 85 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 73 through 74 removed outlier: 6.052A pdb=" N LEU C 66 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLN C 57 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 68 " --> pdb=" O TRP C 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 23 through 25 Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.732A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR B 127 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.732A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 897 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: 1.67 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1812 1.34 - 1.46: 1621 1.46 - 1.58: 2844 1.58 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 6326 Sorted by residual: bond pdb=" CAT 8PR A 702 " pdb=" CAX 8PR A 702 " ideal model delta sigma weight residual 1.509 1.570 -0.061 2.00e-02 2.50e+03 9.45e+00 bond pdb=" CAV 8PR A 702 " pdb=" OAQ 8PR A 702 " ideal model delta sigma weight residual 1.354 1.413 -0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" CAI 8PR A 702 " pdb=" NAN 8PR A 702 " ideal model delta sigma weight residual 1.452 1.504 -0.052 2.00e-02 2.50e+03 6.79e+00 bond pdb=" CAU 8PR A 702 " pdb=" OAP 8PR A 702 " ideal model delta sigma weight residual 1.362 1.413 -0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" CAK 8PR A 702 " pdb=" NAN 8PR A 702 " ideal model delta sigma weight residual 1.451 1.498 -0.047 2.00e-02 2.50e+03 5.56e+00 ... (remaining 6321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 8515 2.20 - 4.40: 80 4.40 - 6.60: 16 6.60 - 8.80: 6 8.80 - 11.00: 2 Bond angle restraints: 8619 Sorted by residual: angle pdb=" CAE 8PR A 702 " pdb=" CAT 8PR A 702 " pdb=" CAX 8PR A 702 " ideal model delta sigma weight residual 120.67 109.67 11.00 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N ARG B 121 " pdb=" CA ARG B 121 " pdb=" C ARG B 121 " ideal model delta sigma weight residual 109.81 117.41 -7.60 2.21e+00 2.05e-01 1.18e+01 angle pdb=" C2 LMT A 705 " pdb=" C3 LMT A 705 " pdb=" C4 LMT A 705 " ideal model delta sigma weight residual 117.09 107.26 9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CAF 8PR A 702 " pdb=" CAT 8PR A 702 " pdb=" CAX 8PR A 702 " ideal model delta sigma weight residual 121.28 130.08 -8.80 3.00e+00 1.11e-01 8.60e+00 angle pdb=" C10 LMT A 705 " pdb=" C9 LMT A 705 " pdb=" C8 LMT A 705 " ideal model delta sigma weight residual 116.03 107.37 8.66 3.00e+00 1.11e-01 8.33e+00 ... (remaining 8614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.14: 3574 29.14 - 58.27: 111 58.27 - 87.41: 2 87.41 - 116.54: 1 116.54 - 145.68: 1 Dihedral angle restraints: 3689 sinusoidal: 1475 harmonic: 2214 Sorted by residual: dihedral pdb=" CA ARG B 121 " pdb=" C ARG B 121 " pdb=" N PRO B 122 " pdb=" CA PRO B 122 " ideal model delta harmonic sigma weight residual 180.00 129.71 50.29 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CAX 8PR A 702 " pdb=" CAM 8PR A 702 " pdb=" CAW 8PR A 702 " pdb=" OAO 8PR A 702 " ideal model delta sinusoidal sigma weight residual 182.60 36.92 145.68 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" CB GLU A 78 " pdb=" CG GLU A 78 " pdb=" CD GLU A 78 " pdb=" OE1 GLU A 78 " ideal model delta sinusoidal sigma weight residual 0.00 89.79 -89.79 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 3686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 727 0.043 - 0.085: 193 0.085 - 0.128: 41 0.128 - 0.171: 1 0.171 - 0.213: 4 Chirality restraints: 966 Sorted by residual: chirality pdb=" C5' LMT A 705 " pdb=" C4' LMT A 705 " pdb=" C6' LMT A 705 " pdb=" O5' LMT A 705 " both_signs ideal model delta sigma weight residual False -2.51 -2.29 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C4' LMT A 705 " pdb=" C3' LMT A 705 " pdb=" C5' LMT A 705 " pdb=" O1B LMT A 705 " both_signs ideal model delta sigma weight residual False -2.55 -2.76 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CAX 8PR A 702 " pdb=" CAJ 8PR A 702 " pdb=" CAT 8PR A 702 " pdb=" CAW 8PR A 702 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 963 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 121 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO B 122 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 287 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.21e+00 pdb=" N PRO A 288 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 130 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO A 131 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " 0.015 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 743 2.75 - 3.29: 6254 3.29 - 3.82: 10369 3.82 - 4.36: 11887 4.36 - 4.90: 20868 Nonbonded interactions: 50121 Sorted by model distance: nonbonded pdb=" O PRO A 571 " pdb=" OG SER A 574 " model vdw 2.212 3.040 nonbonded pdb=" OG SER A 242 " pdb=" O LEU A 248 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR C 56 " pdb=" OE1 GLN C 109 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASP A 328 " pdb=" O4' LMT A 705 " model vdw 2.287 3.040 nonbonded pdb=" OG1 THR C 83 " pdb=" OG1 THR C 94 " model vdw 2.307 3.040 ... (remaining 50116 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.190 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 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 : 0.004 0.061 6331 Z= 0.181 Angle : 0.604 11.004 8631 Z= 0.292 Chirality : 0.040 0.213 966 Planarity : 0.004 0.073 1048 Dihedral : 13.500 145.676 2274 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -3.01 (0.27), residues: 758 helix: -1.15 (0.24), residues: 360 sheet: -2.83 (0.43), residues: 105 loop : -2.61 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 197 HIS 0.006 0.001 HIS C 111 PHE 0.013 0.001 PHE A 380 TYR 0.014 0.001 TYR B 123 ARG 0.002 0.000 ARG A 390 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 2) link_NAG-ASN : angle 0.78022 ( 6) hydrogen bonds : bond 0.17441 ( 306) hydrogen bonds : angle 6.90517 ( 897) SS BOND : bond 0.00314 ( 3) SS BOND : angle 0.37720 ( 6) covalent geometry : bond 0.00370 ( 6326) covalent geometry : angle 0.60374 ( 8619) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.7829 (t80) cc_final: 0.7608 (t80) REVERT: A 270 ILE cc_start: 0.7191 (tp) cc_final: 0.6813 (tp) REVERT: A 271 TRP cc_start: 0.5986 (p-90) cc_final: 0.5555 (p-90) REVERT: A 272 LYS cc_start: 0.8402 (tppp) cc_final: 0.7912 (tptt) REVERT: A 311 PHE cc_start: 0.6600 (m-10) cc_final: 0.6390 (m-80) REVERT: A 316 ASN cc_start: 0.7477 (t0) cc_final: 0.6859 (t0) REVERT: A 615 GLU cc_start: 0.5133 (mp0) cc_final: 0.3315 (pt0) REVERT: C 62 GLN cc_start: 0.6892 (mm-40) cc_final: 0.6364 (mt0) REVERT: C 73 TYR cc_start: 0.8083 (m-80) cc_final: 0.7785 (m-80) REVERT: C 81 ARG cc_start: 0.6620 (tpm170) cc_final: 0.4840 (ptt90) REVERT: C 123 LYS cc_start: 0.6894 (mptt) cc_final: 0.6315 (mtpt) REVERT: B 39 ILE cc_start: 0.6117 (mm) cc_final: 0.5845 (tp) REVERT: B 57 LYS cc_start: 0.7771 (tttt) cc_final: 0.7131 (tttt) REVERT: B 130 GLN cc_start: 0.7601 (pt0) cc_final: 0.7401 (pt0) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1939 time to fit residues: 28.3685 Evaluate side-chains 91 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 111 GLN A 112 ASN A 235 HIS C 26 GLN C 47 GLN C 57 GLN B 54 ASN B 69 ASN B 130 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.195662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.173478 restraints weight = 8023.043| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 3.21 r_work: 0.3924 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6331 Z= 0.136 Angle : 0.548 8.622 8631 Z= 0.283 Chirality : 0.039 0.141 966 Planarity : 0.004 0.078 1048 Dihedral : 7.889 129.256 958 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.54 % Allowed : 10.92 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.57 (0.30), residues: 758 helix: 0.17 (0.26), residues: 369 sheet: -2.21 (0.44), residues: 106 loop : -2.12 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 103 HIS 0.009 0.001 HIS C 111 PHE 0.017 0.001 PHE A 548 TYR 0.035 0.002 TYR A 142 ARG 0.003 0.000 ARG A 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 2) link_NAG-ASN : angle 1.28207 ( 6) hydrogen bonds : bond 0.03984 ( 306) hydrogen bonds : angle 4.76681 ( 897) SS BOND : bond 0.00181 ( 3) SS BOND : angle 0.64088 ( 6) covalent geometry : bond 0.00312 ( 6326) covalent geometry : angle 0.54725 ( 8619) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 176 TYR cc_start: 0.8310 (t80) cc_final: 0.8064 (t80) REVERT: A 204 TRP cc_start: 0.7020 (p90) cc_final: 0.6384 (p90) REVERT: A 270 ILE cc_start: 0.7297 (tp) cc_final: 0.6915 (tp) REVERT: A 271 TRP cc_start: 0.5972 (p-90) cc_final: 0.5545 (p-90) REVERT: A 272 LYS cc_start: 0.8585 (tppp) cc_final: 0.8169 (tptp) REVERT: A 316 ASN cc_start: 0.7723 (t0) cc_final: 0.7100 (t0) REVERT: A 615 GLU cc_start: 0.5314 (mp0) cc_final: 0.3287 (pt0) REVERT: C 56 TYR cc_start: 0.8692 (m-80) cc_final: 0.8281 (m-80) REVERT: C 62 GLN cc_start: 0.7308 (mm-40) cc_final: 0.6710 (mt0) REVERT: C 81 ARG cc_start: 0.7052 (tpm170) cc_final: 0.5249 (ptt90) REVERT: C 123 LYS cc_start: 0.7243 (mptt) cc_final: 0.6595 (mtpt) outliers start: 10 outliers final: 9 residues processed: 85 average time/residue: 0.1948 time to fit residues: 22.6891 Evaluate side-chains 87 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 43 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.198822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.177665 restraints weight = 8030.649| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 3.03 r_work: 0.3942 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6331 Z= 0.127 Angle : 0.533 7.831 8631 Z= 0.276 Chirality : 0.039 0.146 966 Planarity : 0.004 0.078 1048 Dihedral : 7.158 117.162 958 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.31 % Allowed : 12.92 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.98 (0.31), residues: 758 helix: 0.63 (0.27), residues: 373 sheet: -1.75 (0.45), residues: 106 loop : -1.91 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 103 HIS 0.009 0.001 HIS C 111 PHE 0.030 0.001 PHE A 311 TYR 0.022 0.001 TYR A 142 ARG 0.002 0.000 ARG A 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 2) link_NAG-ASN : angle 1.27719 ( 6) hydrogen bonds : bond 0.03670 ( 306) hydrogen bonds : angle 4.44238 ( 897) SS BOND : bond 0.00068 ( 3) SS BOND : angle 0.44572 ( 6) covalent geometry : bond 0.00294 ( 6326) covalent geometry : angle 0.53242 ( 8619) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 176 TYR cc_start: 0.8140 (t80) cc_final: 0.7840 (t80) REVERT: A 204 TRP cc_start: 0.6759 (p90) cc_final: 0.6222 (p90) REVERT: A 270 ILE cc_start: 0.6889 (tp) cc_final: 0.6545 (tp) REVERT: A 316 ASN cc_start: 0.7424 (t0) cc_final: 0.6732 (t0) REVERT: A 507 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6779 (tt) REVERT: A 615 GLU cc_start: 0.5204 (mp0) cc_final: 0.4892 (mm-30) REVERT: C 56 TYR cc_start: 0.8725 (m-80) cc_final: 0.8190 (m-80) REVERT: C 62 GLN cc_start: 0.6936 (mm-40) cc_final: 0.6368 (mt0) REVERT: C 81 ARG cc_start: 0.6894 (tpm170) cc_final: 0.5103 (ptt90) REVERT: C 123 LYS cc_start: 0.7135 (mptt) cc_final: 0.6343 (tttm) outliers start: 15 outliers final: 11 residues processed: 86 average time/residue: 0.1922 time to fit residues: 22.4003 Evaluate side-chains 89 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 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 112 ASN B 54 ASN B 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.197533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.175940 restraints weight = 8069.430| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 3.14 r_work: 0.3926 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6331 Z= 0.124 Angle : 0.521 7.897 8631 Z= 0.271 Chirality : 0.039 0.141 966 Planarity : 0.004 0.077 1048 Dihedral : 6.481 101.595 958 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.15 % Allowed : 15.69 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.61 (0.31), residues: 758 helix: 0.83 (0.27), residues: 374 sheet: -1.30 (0.47), residues: 106 loop : -1.70 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 103 HIS 0.009 0.001 HIS C 111 PHE 0.044 0.002 PHE A 311 TYR 0.023 0.001 TYR A 134 ARG 0.002 0.000 ARG A 241 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 2) link_NAG-ASN : angle 1.18902 ( 6) hydrogen bonds : bond 0.03506 ( 306) hydrogen bonds : angle 4.29475 ( 897) SS BOND : bond 0.00076 ( 3) SS BOND : angle 0.33231 ( 6) covalent geometry : bond 0.00285 ( 6326) covalent geometry : angle 0.52036 ( 8619) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.655 Fit side-chains REVERT: A 176 TYR cc_start: 0.8099 (t80) cc_final: 0.7782 (t80) REVERT: A 204 TRP cc_start: 0.6736 (p90) cc_final: 0.6202 (p90) REVERT: A 241 ARG cc_start: 0.7629 (mtp180) cc_final: 0.7417 (mtp180) REVERT: A 270 ILE cc_start: 0.6785 (tp) cc_final: 0.6466 (tp) REVERT: A 271 TRP cc_start: 0.5671 (p-90) cc_final: 0.5240 (p-90) REVERT: A 316 ASN cc_start: 0.7343 (t0) cc_final: 0.6632 (t0) REVERT: A 606 GLU cc_start: 0.6422 (tt0) cc_final: 0.6162 (tt0) REVERT: A 615 GLU cc_start: 0.5310 (mp0) cc_final: 0.4954 (mm-30) REVERT: C 31 MET cc_start: 0.1739 (mtm) cc_final: 0.1453 (mpp) REVERT: C 62 GLN cc_start: 0.6832 (mm-40) cc_final: 0.6291 (mt0) REVERT: C 81 ARG cc_start: 0.7004 (tpm170) cc_final: 0.5101 (ptt90) REVERT: C 123 LYS cc_start: 0.7093 (mptt) cc_final: 0.6329 (mtpt) outliers start: 14 outliers final: 12 residues processed: 84 average time/residue: 0.1804 time to fit residues: 20.6701 Evaluate side-chains 86 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 0.0070 chunk 66 optimal weight: 0.2980 chunk 69 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 61 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN C 26 GLN B 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.200011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.178421 restraints weight = 7979.513| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 3.13 r_work: 0.3952 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6331 Z= 0.102 Angle : 0.499 7.774 8631 Z= 0.259 Chirality : 0.038 0.135 966 Planarity : 0.004 0.075 1048 Dihedral : 6.060 88.669 958 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.46 % Allowed : 15.69 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.36 (0.31), residues: 758 helix: 1.03 (0.27), residues: 374 sheet: -1.28 (0.47), residues: 106 loop : -1.53 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 103 HIS 0.007 0.001 HIS C 111 PHE 0.035 0.001 PHE A 311 TYR 0.023 0.001 TYR A 134 ARG 0.002 0.000 ARG A 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00242 ( 2) link_NAG-ASN : angle 1.09387 ( 6) hydrogen bonds : bond 0.03282 ( 306) hydrogen bonds : angle 4.18725 ( 897) SS BOND : bond 0.00196 ( 3) SS BOND : angle 0.40865 ( 6) covalent geometry : bond 0.00228 ( 6326) covalent geometry : angle 0.49853 ( 8619) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 124 MET cc_start: 0.7242 (mmp) cc_final: 0.6923 (mmp) REVERT: A 135 MET cc_start: 0.8630 (ttp) cc_final: 0.8338 (ttp) REVERT: A 204 TRP cc_start: 0.6623 (p90) cc_final: 0.6071 (p90) REVERT: A 270 ILE cc_start: 0.6690 (tp) cc_final: 0.6389 (tp) REVERT: A 271 TRP cc_start: 0.5651 (p-90) cc_final: 0.5189 (p-90) REVERT: A 316 ASN cc_start: 0.7222 (t0) cc_final: 0.6499 (t0) REVERT: A 507 ILE cc_start: 0.6941 (OUTLIER) cc_final: 0.6665 (tt) REVERT: A 606 GLU cc_start: 0.6354 (tt0) cc_final: 0.6072 (tt0) REVERT: A 615 GLU cc_start: 0.5248 (mp0) cc_final: 0.4914 (mm-30) REVERT: C 31 MET cc_start: 0.1719 (mtm) cc_final: 0.1436 (mpp) REVERT: C 62 GLN cc_start: 0.6708 (mm-40) cc_final: 0.6208 (mt0) REVERT: C 81 ARG cc_start: 0.6940 (tpm170) cc_final: 0.5051 (ptt90) REVERT: C 123 LYS cc_start: 0.7028 (mptt) cc_final: 0.6263 (tttm) outliers start: 16 outliers final: 11 residues processed: 80 average time/residue: 0.1768 time to fit residues: 19.3389 Evaluate side-chains 81 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 24 optimal weight: 0.0000 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 37 optimal weight: 0.3980 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.200212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.178709 restraints weight = 7961.848| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.13 r_work: 0.3950 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6331 Z= 0.101 Angle : 0.493 7.761 8631 Z= 0.256 Chirality : 0.038 0.131 966 Planarity : 0.004 0.076 1048 Dihedral : 5.781 74.356 958 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.62 % Allowed : 16.92 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.15 (0.32), residues: 758 helix: 1.13 (0.27), residues: 375 sheet: -1.08 (0.49), residues: 106 loop : -1.36 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 103 HIS 0.007 0.001 HIS C 111 PHE 0.033 0.001 PHE A 311 TYR 0.018 0.001 TYR A 134 ARG 0.002 0.000 ARG A 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 2) link_NAG-ASN : angle 1.05996 ( 6) hydrogen bonds : bond 0.03181 ( 306) hydrogen bonds : angle 4.11978 ( 897) SS BOND : bond 0.00110 ( 3) SS BOND : angle 0.27865 ( 6) covalent geometry : bond 0.00229 ( 6326) covalent geometry : angle 0.49242 ( 8619) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 204 TRP cc_start: 0.6947 (p90) cc_final: 0.6272 (p90) REVERT: A 270 ILE cc_start: 0.7139 (tp) cc_final: 0.6766 (tp) REVERT: A 271 TRP cc_start: 0.5948 (p-90) cc_final: 0.5514 (p-90) REVERT: A 316 ASN cc_start: 0.7561 (t0) cc_final: 0.6861 (t0) REVERT: A 507 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7110 (tt) REVERT: A 615 GLU cc_start: 0.5404 (mp0) cc_final: 0.4925 (mp0) REVERT: C 31 MET cc_start: 0.1772 (mtm) cc_final: 0.1518 (mpp) REVERT: C 62 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6679 (mt0) REVERT: C 81 ARG cc_start: 0.7114 (tpm170) cc_final: 0.5321 (ptt90) REVERT: C 123 LYS cc_start: 0.7201 (mptt) cc_final: 0.6545 (tttm) REVERT: B 53 MET cc_start: 0.7491 (mmm) cc_final: 0.7195 (tpt) outliers start: 17 outliers final: 12 residues processed: 87 average time/residue: 0.1728 time to fit residues: 20.5347 Evaluate side-chains 87 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 0.0970 chunk 45 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 205 ASN C 26 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.199955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.178351 restraints weight = 7964.061| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 3.11 r_work: 0.3942 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6331 Z= 0.115 Angle : 0.521 7.820 8631 Z= 0.270 Chirality : 0.039 0.129 966 Planarity : 0.004 0.077 1048 Dihedral : 5.787 69.549 958 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.46 % Allowed : 18.31 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.09 (0.32), residues: 758 helix: 1.13 (0.27), residues: 376 sheet: -1.02 (0.49), residues: 106 loop : -1.27 (0.40), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 103 HIS 0.008 0.001 HIS C 111 PHE 0.031 0.001 PHE A 311 TYR 0.023 0.001 TYR A 176 ARG 0.002 0.000 ARG A 241 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 2) link_NAG-ASN : angle 1.12363 ( 6) hydrogen bonds : bond 0.03248 ( 306) hydrogen bonds : angle 4.10558 ( 897) SS BOND : bond 0.00090 ( 3) SS BOND : angle 0.37263 ( 6) covalent geometry : bond 0.00266 ( 6326) covalent geometry : angle 0.52041 ( 8619) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 204 TRP cc_start: 0.6565 (p90) cc_final: 0.6142 (p90) REVERT: A 216 ASP cc_start: 0.6918 (t0) cc_final: 0.6469 (t0) REVERT: A 270 ILE cc_start: 0.6702 (tp) cc_final: 0.6405 (tp) REVERT: A 271 TRP cc_start: 0.5624 (p-90) cc_final: 0.5155 (p-90) REVERT: A 316 ASN cc_start: 0.7197 (t0) cc_final: 0.6458 (t0) REVERT: A 507 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6691 (tt) REVERT: A 606 GLU cc_start: 0.6317 (tt0) cc_final: 0.6013 (tt0) REVERT: A 615 GLU cc_start: 0.5354 (mp0) cc_final: 0.4848 (mp0) REVERT: C 31 MET cc_start: 0.1582 (mtm) cc_final: 0.1309 (mpp) REVERT: C 62 GLN cc_start: 0.6763 (mm-40) cc_final: 0.6273 (mt0) REVERT: C 81 ARG cc_start: 0.6962 (tpm170) cc_final: 0.5080 (ptt90) REVERT: C 123 LYS cc_start: 0.7027 (mptt) cc_final: 0.6297 (tttm) REVERT: B 53 MET cc_start: 0.7096 (mmm) cc_final: 0.6810 (tpt) outliers start: 16 outliers final: 11 residues processed: 88 average time/residue: 0.1596 time to fit residues: 19.4469 Evaluate side-chains 85 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 45 optimal weight: 0.0970 chunk 70 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 205 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 = 0.4241 r_free = 0.4241 target = 0.199485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.177722 restraints weight = 7907.901| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 3.12 r_work: 0.3917 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6331 Z= 0.112 Angle : 0.523 7.807 8631 Z= 0.269 Chirality : 0.038 0.127 966 Planarity : 0.004 0.077 1048 Dihedral : 5.791 64.997 958 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.31 % Allowed : 19.08 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: 0.03 (0.32), residues: 758 helix: 1.19 (0.27), residues: 373 sheet: -0.93 (0.49), residues: 106 loop : -1.15 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 197 HIS 0.008 0.001 HIS C 111 PHE 0.030 0.001 PHE A 311 TYR 0.021 0.001 TYR A 176 ARG 0.003 0.000 ARG A 390 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 2) link_NAG-ASN : angle 1.00335 ( 6) hydrogen bonds : bond 0.03259 ( 306) hydrogen bonds : angle 4.12513 ( 897) SS BOND : bond 0.00212 ( 3) SS BOND : angle 0.50315 ( 6) covalent geometry : bond 0.00260 ( 6326) covalent geometry : angle 0.52235 ( 8619) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 204 TRP cc_start: 0.7135 (p90) cc_final: 0.6427 (p90) REVERT: A 216 ASP cc_start: 0.7216 (t0) cc_final: 0.6834 (t0) REVERT: A 270 ILE cc_start: 0.7191 (tp) cc_final: 0.6820 (tp) REVERT: A 271 TRP cc_start: 0.5975 (p-90) cc_final: 0.5566 (p-90) REVERT: A 316 ASN cc_start: 0.7662 (t0) cc_final: 0.6959 (t0) REVERT: A 507 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7162 (tt) REVERT: A 606 GLU cc_start: 0.6201 (tt0) cc_final: 0.5876 (tt0) REVERT: A 615 GLU cc_start: 0.5517 (mp0) cc_final: 0.4993 (mp0) REVERT: C 62 GLN cc_start: 0.7340 (mm-40) cc_final: 0.6773 (mt0) REVERT: C 81 ARG cc_start: 0.7161 (tpm170) cc_final: 0.5374 (ptt90) REVERT: C 123 LYS cc_start: 0.7211 (mptt) cc_final: 0.6613 (tttm) REVERT: B 46 TYR cc_start: 0.5962 (m-80) cc_final: 0.5684 (m-80) REVERT: B 53 MET cc_start: 0.7576 (mmm) cc_final: 0.7267 (tpt) outliers start: 15 outliers final: 12 residues processed: 82 average time/residue: 0.1725 time to fit residues: 19.5166 Evaluate side-chains 86 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 51 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 205 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 = 0.4235 r_free = 0.4235 target = 0.198663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.176803 restraints weight = 8047.672| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 3.15 r_work: 0.3953 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6331 Z= 0.116 Angle : 0.522 7.811 8631 Z= 0.270 Chirality : 0.039 0.128 966 Planarity : 0.004 0.077 1048 Dihedral : 5.798 61.115 958 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.31 % Allowed : 19.23 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.07 (0.32), residues: 758 helix: 1.08 (0.27), residues: 381 sheet: -0.85 (0.50), residues: 106 loop : -1.27 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 197 HIS 0.008 0.001 HIS C 111 PHE 0.029 0.001 PHE A 311 TYR 0.020 0.001 TYR A 176 ARG 0.004 0.000 ARG A 390 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 2) link_NAG-ASN : angle 0.96389 ( 6) hydrogen bonds : bond 0.03296 ( 306) hydrogen bonds : angle 4.09781 ( 897) SS BOND : bond 0.00117 ( 3) SS BOND : angle 0.45307 ( 6) covalent geometry : bond 0.00266 ( 6326) covalent geometry : angle 0.52120 ( 8619) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 204 TRP cc_start: 0.6895 (p90) cc_final: 0.6196 (p90) REVERT: A 216 ASP cc_start: 0.7018 (t0) cc_final: 0.6559 (t0) REVERT: A 270 ILE cc_start: 0.6835 (tp) cc_final: 0.6527 (tp) REVERT: A 271 TRP cc_start: 0.5725 (p-90) cc_final: 0.5273 (p-90) REVERT: A 316 ASN cc_start: 0.7318 (t0) cc_final: 0.6578 (t0) REVERT: A 507 ILE cc_start: 0.7108 (OUTLIER) cc_final: 0.6826 (tt) REVERT: A 606 GLU cc_start: 0.6319 (tt0) cc_final: 0.6015 (tt0) REVERT: A 615 GLU cc_start: 0.5421 (mp0) cc_final: 0.4878 (mp0) REVERT: C 31 MET cc_start: 0.1727 (mtm) cc_final: 0.1507 (mpp) REVERT: C 62 GLN cc_start: 0.6925 (mm-40) cc_final: 0.6406 (mt0) REVERT: C 81 ARG cc_start: 0.7058 (tpm170) cc_final: 0.5165 (ptt90) REVERT: C 123 LYS cc_start: 0.7127 (mptt) cc_final: 0.6452 (mtpt) REVERT: B 46 TYR cc_start: 0.6155 (m-80) cc_final: 0.5821 (m-80) REVERT: B 53 MET cc_start: 0.7251 (mmm) cc_final: 0.6952 (tpt) REVERT: B 123 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6012 (t80) outliers start: 15 outliers final: 12 residues processed: 83 average time/residue: 0.2044 time to fit residues: 23.5960 Evaluate side-chains 86 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 34 optimal weight: 0.0370 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 0.0370 chunk 14 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 13 optimal weight: 0.0050 chunk 32 optimal weight: 1.9990 overall best weight: 0.3150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 205 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 = 0.4268 r_free = 0.4268 target = 0.202637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.180940 restraints weight = 7979.335| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 3.14 r_work: 0.3942 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6331 Z= 0.095 Angle : 0.508 7.590 8631 Z= 0.261 Chirality : 0.038 0.127 966 Planarity : 0.004 0.075 1048 Dihedral : 5.619 56.344 958 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.15 % Allowed : 19.38 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: 0.16 (0.32), residues: 758 helix: 1.31 (0.27), residues: 373 sheet: -0.86 (0.49), residues: 106 loop : -1.10 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 55 HIS 0.006 0.001 HIS C 111 PHE 0.030 0.001 PHE A 311 TYR 0.021 0.001 TYR A 176 ARG 0.003 0.000 ARG A 390 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 2) link_NAG-ASN : angle 0.92962 ( 6) hydrogen bonds : bond 0.03079 ( 306) hydrogen bonds : angle 4.04387 ( 897) SS BOND : bond 0.00142 ( 3) SS BOND : angle 0.39616 ( 6) covalent geometry : bond 0.00210 ( 6326) covalent geometry : angle 0.50718 ( 8619) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.7191 (t0) cc_final: 0.6711 (t0) REVERT: A 270 ILE cc_start: 0.7153 (tp) cc_final: 0.6765 (tp) REVERT: A 271 TRP cc_start: 0.5965 (p-90) cc_final: 0.5760 (p-90) REVERT: A 316 ASN cc_start: 0.7598 (t0) cc_final: 0.6898 (t0) REVERT: A 440 PHE cc_start: 0.6797 (m-10) cc_final: 0.6075 (m-80) REVERT: A 507 ILE cc_start: 0.7429 (OUTLIER) cc_final: 0.7134 (tt) REVERT: A 615 GLU cc_start: 0.5449 (mp0) cc_final: 0.4936 (mp0) REVERT: C 48 ASP cc_start: 0.7401 (t0) cc_final: 0.7184 (t0) REVERT: C 62 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6700 (mt0) REVERT: C 81 ARG cc_start: 0.7162 (tpm170) cc_final: 0.5377 (ptt90) REVERT: C 123 LYS cc_start: 0.7219 (mptt) cc_final: 0.6669 (tttm) REVERT: B 46 TYR cc_start: 0.5968 (m-80) cc_final: 0.5706 (m-80) REVERT: B 123 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6372 (t80) outliers start: 14 outliers final: 10 residues processed: 85 average time/residue: 0.1841 time to fit residues: 22.1028 Evaluate side-chains 87 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 TYR Chi-restraints excluded: chain B residue 133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN B 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.196374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.174496 restraints weight = 8069.203| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 3.15 r_work: 0.3883 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6331 Z= 0.141 Angle : 0.548 8.126 8631 Z= 0.284 Chirality : 0.040 0.131 966 Planarity : 0.004 0.080 1048 Dihedral : 5.803 56.006 958 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.00 % Allowed : 20.00 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -0.09 (0.32), residues: 758 helix: 1.04 (0.27), residues: 382 sheet: -0.84 (0.49), residues: 106 loop : -1.27 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.010 0.002 HIS C 111 PHE 0.030 0.002 PHE A 311 TYR 0.022 0.002 TYR A 134 ARG 0.004 0.000 ARG A 390 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 2) link_NAG-ASN : angle 0.94095 ( 6) hydrogen bonds : bond 0.03509 ( 306) hydrogen bonds : angle 4.12313 ( 897) SS BOND : bond 0.00352 ( 3) SS BOND : angle 0.79580 ( 6) covalent geometry : bond 0.00332 ( 6326) covalent geometry : angle 0.54747 ( 8619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3494.01 seconds wall clock time: 63 minutes 16.76 seconds (3796.76 seconds total)